├── README.md
├── Structural_Variant_Sets
    ├── Nonredundant_Structural_Variants
    │   ├── Deletions
    │   │   └── README.md
    │   ├── Duplications
    │   │   └── README.md
    │   ├── Insertions
    │   │   └── README.md
    │   ├── QuickStart.md
    │   ├── README.md
    │   └── ToolGuide.md
    └── README.md
├── images
    ├── NR_sv_chr1.PNG
    ├── NR_sv_chr1_detail.PNG
    ├── NR_sv_chr1_zoom.PNG
    ├── galaxy.PNG
    ├── galaxy_vcf.PNG
    ├── stub
    ├── ucsc_browser.PNG
    └── ucsc_browser_ins.PNG
├── nr_stats_tables
    ├── ftp_manifest-table4.20191104.inc.md
    └── test
├── specs
    ├── README.md
    ├── dbVar.xsd
    ├── dbVarSubmissionTemplate_v3.4.xlsx
    └── dbVarSubmissionTemplate_v3.5.xlsx
└── tutorials
    └── README.md


/README.md:
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 1 | # dbVar (https://www.ncbi.nlm.nih.gov/dbvar)
 2 | ## dbVar is NCBI's database of human genomic structural variation – insertions, deletions, duplications, inversions, mobile elements, and translocations
 3 | ============================
 4 | 
 5 | ### directory layout
 6 | 
 7 |     .
 8 |     +-- Structural_Variant_Sets              # dbVar Reference SV Project & Data
 9 |     +-- specs                                # dbVar Design and Schema Specifications     
10 |     +-- tutorials                            # Initial dir and README setup
11 |     +-- README.md
12 | 


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/Structural_Variant_Sets/Nonredundant_Structural_Variants/Deletions/README.md:
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  1 | # dbVar Human Nonredundant Structural Variants – Deletions
  2 | 
  3 | ### Work in progress - data subject to change
  4 | 
  5 | Documentation updated:  11/27/2019
  6 | 
  7 | ## Data Summary
  8 | 
  9 | <h3>
 10 | Deletions</h3>
 11 | <table>
 12 | <tbody>
 13 | <tr>
 14 | <th>Type and FTP Directory</th>
 15 | <th>GRCh37</th>
 16 | <th>GRCh38</th>
 17 | <tr>
 18 | <td>All</td>
 19 | <td>2,520,481</td>
 20 | <td>2,508,155</td>
 21 | </tr>
 22 | <tr>
 23 | <td>Common</td>
 24 | <td>211,888</td>
 25 | <td>211,465</td>
 26 | </tr>
 27 | <tr>
 28 | <td>Pathogenic</td>
 29 | <td>11,296</td>
 30 | <td>11,105</td>
 31 | </tr>
 32 | <tr>
 33 | <td>Somatic</td>
 34 | <td>23,360</td>
 35 | <td>23,319</td>
 36 | </tr>
 37 | </tbody>
 38 | </table>
 39 | 
 40 | All files are available in **bed**, **bedpe**, and **tsv** formats:
 41 | 
 42 | [https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/#github)
 43 | 
 44 | The variant types in the NR "deletions" files are:
 45 | 
 46 |  * alu_deletion
 47 |  * copy_number_loss
 48 |  * deletion
 49 |  * herv_deletion
 50 |  * line1_deletion
 51 |  * sva_deletion
 52 |  
 53 |  
 54 | ## Records in the NR SV deletions files
 55 | 
 56 | ### Please note:
 57 | 
 58 | * The fields type, method, analysis, platform, variant, study, clinical_significance, clinvar_accession, and gene may contain multiple values.  
 59 | * Each of the values is associated with one or more calls found in the variant field.
 60 | * The values in the variant field are "dbVar call accessions".
 61 | 
 62 | * Records in the NR SV deletions files contain the following tab-separated fields.
 63 | 
 64 | | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clinical_assertion | clinvar_accession | bin_size
 65 | 
 66 | 
 67 | ## Example record 1:
 68 |   
 69 | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clinical_assertion | clinvar_accession | bin_size  
 70 | ----|-----------------|----------------|---------------|--------------|--------|----------|----------|-------|---------|--------------------|------------------|------
 71 | X | 153293294 | 153296201 | 1 | deletion | Curated | Curated | NA | LSDB_submitted_variants | nssv7487065 | Pathogenic | SCV000222455 | medium
 72 |  
 73 | ### Explanation:
 74 | 
 75 | * The non-redundant coordinates for this record in dbVar are chr1, with
 76 | an outermost start of 10001 and outermost stop of 1535693.
 77 | 
 78 | * The SV_count of 1 indicates there is only one SV with an exact match to the
 79 | given placement.  This count does not include SVs with a partial match.
 80 | 
 81 | * The variant_call_type is "deletion".
 82 | 
 83 | * The method and the analysis indicate how the one variant was evaluated.
 84 | 
 85 | * NA indicates the no platform was submitted for this variant.
 86 | 
 87 | * LSDB_submitted_variants is the study name as found in dbVar.
 88 | 
 89 | * The dbVar variant_accession is "nssv7487065".
 90 | 
 91 | * The clinical_significance is "Pathogenic"
 92 | 
 93 | * The variant has an accession in ClinVar of SCV000222455
 94 | 
 95 | * bin_size = small (length < 50 bp), medium (< 1000000), large (>= 1000000). Length = outermost_stop - outermost_start + 1.
 96 | 
 97 | * URLs using the study name accession or variant_accession can be created to access the data
 98 | in dbVar, e.g.:
 99 | https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd103/  
100 | https://www.ncbi.nlm.nih.gov/dbvar/?term=nssv7487065
101 | 
102 | * From the latter page you may click on the "Variant Region ID" on the left to see
103 | the variant's region in the NCBI Variation Viewer at:
104 | https://www.ncbi.nlm.nih.gov/dbvar/variants/nsv1197457/
105 | 
106 | * The SCV accession can be used to find the record in ClinVar by searching on ClinVar's home page:
107 | https://www.ncbi.nlm.nih.gov/clinvar/
108 | 
109 | ## Example record 2:
110 | 
111 | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clinical_assertion | clinvar_accession | bin_size  
112 | ----|-----------------|----------------|---------------|--------------|--------|----------|----------|-------|---------|--------------------|------------------|----- 
113 | 1 | 72300544 | 72346418 | 7 | copy_number_loss;deletion | Oligo_aCGH;Sequencing | Probe_signal_intensity;Read_depth | Agilent 24M aCGH;Illumina IIx | Park2010;Ju2010 | nssv1423530:nssv1425248:nssv1428032:nssv1428830:nssv1434173:nssv1439464:nssv1420391 |   |   | medium
114 | 
115 | ### Explanation:
116 | 
117 | * This is a more complicated example deletion NR record containing multiple
118 | variants with multiple types, methods, and analyses from multiple studies, using
119 | multiple platforms.  This record does not contain clinical_significance or a 
120 | ClinVar accession.
121 | 
122 | # Questions or feedback
123 | 
124 | * Please email dbvar@ncbi.nlm.nih.gov or create an issue on this GitHub page.
125 | 
126 | # Thanks!
127 | 
128 | Thanks for your interest in the dbVar human "non-redundant structural variations" (nr SVs)
129 | data files from NCBI.
130 | 
131 | Please check back for updates soon.
132 | 


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/Structural_Variant_Sets/Nonredundant_Structural_Variants/Duplications/README.md:
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  1 | # dbVar Human Nonredundant Structural Variants – Duplications
  2 | 
  3 | ### Work in progress - data subject to change
  4 | 
  5 | Documentation updated:  11/27/2019
  6 | 
  7 | ## Data Summary
  8 | 
  9 | <h3>
 10 | Duplications</h3>
 11 | <table>
 12 | <tbody>
 13 | <tr>
 14 | <th>Type and FTP Directory</th>
 15 | <th>GRCh37</th>
 16 | <th>GRCh38</th>
 17 | <tr>
 18 | <td>All</td>
 19 | <td>418,648</td>
 20 | <td>408,362</td>
 21 | </tr>
 22 | <tr>
 23 | <td>Common</td>
 24 | <td>59,576</td>
 25 | <td>59,150</td>
 26 | </tr>
 27 | <tr>
 28 | <td>Pathogenic</td>
 29 | <td>4,337</td>
 30 | <td>4,206</td>
 31 | </tr>
 32 | <tr>
 33 | <td>Somatic</td>
 34 | <td>15,103</td>
 35 | <td>15,077</td>
 36 | </tr>
 37 | </tbody>
 38 | </table>
 39 | 
 40 | All files are available in **bed**, **bedpe**, and **tsv** formats:
 41 | 
 42 | [https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications/](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications/#github)
 43 | 
 44 | The variant types in the NR "duplications" files are:
 45 | 
 46 |  * copy_number_gain
 47 |  * copy_number_variation
 48 |  * duplication
 49 |  * tandem_duplication
 50 | 
 51 | ## Records in the NR SV duplications files
 52 | 
 53 | ### Please note:
 54 | 
 55 | * The fields type, method, analysis, platform, variant, study, clinical_significance, clinvar_accession, and gene may contain multiple values.
 56 | * Each of the values is associated with one or more calls found in the variant field.
 57 | * The values in the variant field are "dbVar call accessions".
 58 | 
 59 | * Records in the NR SV duplications files contain the following tab-separated fields.
 60 | 
 61 | | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clinical_assertion | clinvar_accession
 62 | 
 63 | 
 64 | ## Example record 1:
 65 | 
 66 | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clinical_assertion | clinvar_accession | bin_size
 67 | ----|-----------------|----------------|---------------|--------------|--------|----------|----------|-------|---------|--------------------|------------------|------
 68 | 15 | 90243115 | 90477618 | 1 | copy_number_gain | Oligo_aCGH | Probe_signal_intensity | NA | ClinGen_Laboratory-Submitted | nssv13652018 | Uncertain significance | SCV000495160 | medium
 69 | 
 70 | ### Explanation:
 71 | 
 72 | * The non-redundant coordinates for this record in dbVar are chr15, with
 73 | an outermost start of 90243115 and outermost stop of 90477618.
 74 | 
 75 | * The variant_count of 1 indicates there is only one ssv with an exact match to
 76 | the given placement.  This count does not include SVs with a partial match.
 77 | 
 78 | * The variant_call_type is "copy_number_gain".
 79 | 
 80 | * The method and the analysis indicate how the one variant was evaluated.
 81 | 
 82 | * NA indicates the no platform was submitted for this variant.
 83 | 
 84 | * ClinGen_Laboratory-Submitted is the study name as found in dbVar.
 85 | 
 86 | * The dbVar variant_accession is "nssv13652018".
 87 | 
 88 | * The clinical_significance is "Uncertain significance"
 89 | 
 90 | * The variant has an accession in ClinVar of SCV000495160
 91 | 
 92 | * bin_size = small (length < 50 bp), medium (<1000000), large (>= 1000000). Length = outermost_stop - outermost_start + 1.
 93 | 
 94 | * URLs using the study name accession or variant_accession can be created to access the data
 95 | in dbVar, e.g.:
 96 | https://www.ncbi.nlm.nih.gov/dbvar/?term=ClinGen_Laboratory-Submitted
 97 | https://www.ncbi.nlm.nih.gov/dbvar/?term=nssv13652018
 98 | 
 99 | * From the latter page you may click on the "Variant Region ID" on the left to see
100 | the variant's region in the NCBI Variation Viewer at:
101 | https://www.ncbi.nlm.nih.gov/dbvar/variants/nsv2769232/
102 | 
103 | * The SCV accession can be used to find the record in ClinVar by searching on ClinVar's home page:
104 | https://www.ncbi.nlm.nih.gov/clinvar/
105 | 
106 | ## Example record 2:
107 | 
108 | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clinical_assertion | clinvar_accession | bin_size 
109 | ----|-----------------|----------------|---------------|--------------|--------|----------|----------|-------|---------|--------------------|------------------|-----
110 | 8 | 75857739 | 75858539 | 2 | duplication;tandem_duplication | Sequencing | Split_read_and_paired-end_mapping;Read_depth_and_paired-end_mapping | Illumina HiSeq X Ten;Illumina HiSeq 2000 | Wong2016;Alsmadi2014 | essv26064592;nssv3988418 |  |  | medium
111 | 
112 | ### Explanation:
113 | 
114 | * This is a more complicated example duplication NR record containing multiple
115 | variants with multiple types, methods, and analyses from multiple studies, using
116 | multiple platforms.  This record does not contain clinical_significance or a
117 | ClinVar accession.
118 | 
119 | # Questions or feedback
120 | 
121 | * Please email dbvar@ncbi.nlm.nih.gov or create an issue on this GitHub page.
122 | 
123 | # Thanks!
124 | 
125 | Thanks for your interest in the dbVar human "non-redundant structural variations" (NR SVs)
126 | data files from NCBI.
127 | 
128 | Please check back for updates soon.
129 | 


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/Structural_Variant_Sets/Nonredundant_Structural_Variants/Insertions/README.md:
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  1 | # dbVar Human Nonredundant Structural Variants – Insertions
  2 | 
  3 | ### Work in progress - data subject to change
  4 | 
  5 | Documentation updated:  11/27/2019
  6 | 
  7 | ## Data Summary
  8 | 
  9 | <h3>
 10 | Insertions</h3>
 11 | <table>
 12 | <tbody>
 13 | <tr>
 14 | <th>Type and FTP Directory</th>
 15 | <th>GRCh37</th>
 16 | <th>GRCh38</th>
 17 | <tr>
 18 | <td>All</td>
 19 | <td>1,305,137</td>
 20 | <td>1,309,867</td>
 21 | </tr>
 22 | <tr>
 23 | <td>Common</td>
 24 | <td>124,902</td>
 25 | <td>124,833</td>
 26 | </tr>
 27 | <tr>
 28 | <td>Pathogenic</td>
 29 | <td>71</td>
 30 | <td>71</td>
 31 | </tr>
 32 | <tr>
 33 | <td>Somatic</td>
 34 | <td>0</td>
 35 | <td>0</td>
 36 | </tr>
 37 | </tbody>
 38 | </table>
 39 | 
 40 | 
 41 | All files are available in **bed**, **bedpe**, and **tsv** formats:
 42 | 
 43 | [https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions/](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions/#github)
 44 | 
 45 | The variant types in the NR "insertions" files are:
 46 | 
 47 |  * alu_insertion
 48 |  * insertion
 49 |  * line1_insertion
 50 |  * mobile_element_insertion
 51 |  * novel_sequence_insertion
 52 |  * sva_insertion
 53 | 
 54 | ## Records in NR SV insertions files
 55 | 
 56 | ### Please note:
 57 | 
 58 | * The fields type, method, analysis, platform, variant, study, clinical_significance, clinvar_accession, and gene may contain multiple values.
 59 | * Each of the values is associated with one or more calls found in the variant field.
 60 | * The values in the variant field are "dbVar call accessions".
 61 | 
 62 | * Records in the NR SV insertions files contain the following tab-separated fields.
 63 | 
 64 | | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clinical_assertion | clinvar_accession | min_insertion_length | max_insertion_length | 
 65 | 
 66 | 
 67 | ## Example record 1:
 68 | 
 69 | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clinical_assertion | clinvar_accession | bin_size | min_insertion_length | max_insertion_length |   
 70 | ----|-----------------|----------------|---------------|--------------|--------|----------|----------|-------|---------|-----------------------------------|-------------|------|----------------------|----------------------|   
 71 | 1 | 370037 | 370038 | 1 | insertion | Sequencing | Local_sequence_assembly | NA | Fan2017 | nssv14027289 | | | small | 94 | 94
 72 | 
 73 | ### Explanation:
 74 | 
 75 | * The non-redundant coordinates for this record in dbVar are chr1, with
 76 | an outermost start of 370037 and outermost stop of 370038.
 77 | 
 78 | * The SV_count of 1 indicates there is only one SV with an exact match to the
 79 | given placement.  This count does not include SVs with a partial match.
 80 | 
 81 | * The variant_call_type is "insertion".
 82 | 
 83 | * The method of "Sequencing" and the analysis of "Local_sequence_assembly"
 84 | indicate how the variant was evaluated.
 85 | 
 86 | * 94 indicates the minimum insertion length, which is the same as the maximum insertion length since there is only one SV at this set of NR coordinates.
 87 | 
 88 | * NA indicates the no platform was specified for this variant.
 89 | 
 90 | * Fan2017 is the study name as found in dbVar.
 91 | 
 92 | * The dbVar variant_accession is "nssv14027289".
 93 | 
 94 | The clinical_assertion is not provided for this variant.
 95 | 
 96 | There is no clinvar_accession for this variant
 97 | 
 98 | bin_size = small (length < 50 bp), medium (< 1000000), large (>= 1000000), where length = outermost_stop - outermost_start + 1.
 99 | 
100 | * URLs using the study name or variant_accession can be created to access the data
101 | in dbVar, e.g.:
102 | https://www.ncbi.nlm.nih.gov/dbvar/?term=Fan2017  
103 | https://www.ncbi.nlm.nih.gov/dbvar/?term=nssv14027289
104 | 
105 | * From the latter page you may click on the "Variant Region ID" on the left to see
106 | the variant's region in the NCBI Variation Viewer at:
107 | https://www.ncbi.nlm.nih.gov/dbvar/variants/nsv3056167/
108 | 
109 | ## Example record 2:
110 | 
111 | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clinical_assertion | clinvar_accession | bin_size | min_insertion_length | max_insertion_length 
112 | ----|-----------------|----------------|---------------|--------------|--------|----------|----------|-------|---------|-----------------------------------|-----------|--------|----------------------|----------------------|   
113 | 1 | 147236943 | 147236943 | 2 | insertion;line1_insertion | Sequencing | Sequence_alignment;Split_read_and_paired-end_mapping | Sanger Sequencing;HiSeq 2000 | Levy2007;Gardner2017 | essv4283099;nssv14075648 |  |  | small | 10 | 6014
114 | 
115 | ### Explanation:
116 | 
117 | * This is a more complicated example insertion NR record containing multiple variants with multiple variant_types, methods, analyses, studies, platforms, and insertion_lengths.
118 | 
119 | # Questions or feedback
120 | 
121 | * Please email dbvar@ncbi.nlm.nih.gov or create an issue on this GitHub page.
122 | 
123 | # Thanks!
124 | 
125 | Thanks for your interest in the dbVar human "non-redundant structural variations" (nr SVs)
126 | data files from NCBI.
127 | 
128 | Please check back for updates soon.
129 | 


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/Structural_Variant_Sets/Nonredundant_Structural_Variants/QuickStart.md:
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  1 | # Quick Start
  2 | 
  3 | 
  4 | ## A guide to using dbVar non-redundant structural variant (NR-SV) data and annotations
  5 | 
  6 | **Updated** September 12, 2018
  7 | 
  8 | 
  9 | ----------
 10 | 
 11 | 
 12 | 
 13 | The ***Use Cases*** below illustrate some of the ways dbVar NR SV data and associated annotations can be used. Please send feedback and any questions to dbvar-dev@ncbi.nlm.nih.gov.
 14 | 
 15 | dbVar NR data are provided in GRCh37 and GRCh38 coordinates in TSV, BED, and BEDPE formats. Please choose the file(s) best suited your application. For example, BED files are easy to compute on but are lightweight and lack metadata such as clinical assertions that may be useful to your analysis.
 16 | 
 17 | **NOTE:** At the present time not all clinical SV in ClinVar have yet been ported to dbVar. In addition, clinical assertions contained in NR-SV datasets are not diagnostic and should be interpreted with caution. For more information please visit [ClinVar's Clinical Significance](https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/) informational page.
 18 | 
 19 | #### Disclaimer
 20 | 
 21 | The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. NIH does not independently verify the submitted information. If you have questions about the information contained on this website, please see a health care professional. More information about [NCBI's disclaimer policy](https://www.ncbi.nlm.nih.gov/About/disclaimer.html) is available.
 22 | 
 23 | 
 24 | 
 25 | 
 26 | ----------
 27 | 
 28 | ## Use Cases:
 29 | <!-- TOC depthFrom:3 depthTo:3 withLinks:1 updateOnSave:1 orderedList:0 -->
 30 | 
 31 | - [Obtain human clinically-relevant CNVs](#obtain-human-clinically-relevant-cnvs)
 32 | - [Find overlaps between NR-SV and candidate structural variants](#find-overlaps-between-nr-sv-and-candidate-structural-variants)
 33 | - [Find overlaps between NR SVs and annotation datasets](#find-overlaps-between-nr-svs-and-annotation-datasets)
 34 | 
 35 | <!-- /TOC -->
 36 | 
 37 | ----------
 38 | 
 39 | ### Obtain human clinically-relevant CNVs
 40 | 
 41 | #### Objectives:
 42 | * Group NR SV records with clinically-relevant CNVs by assembly and by type
 43 | * To obtain clinically-relevant NR SVs in bedpe format so they may be used for further investigation, e.g., to:
 44 |   * determine genome locations where pathogenic copy number loss variants are found in dbVar
 45 |   * determine overlaps between these these variants and a candidate set of variants
 46 | 
 47 | #### Summary of Results:
 48 | Using the process described in this use case the following results were obtained on Aug 20, 2018:
 49 | 
 50 | Two files of NR SVs, each NR SV containing at least one clinically relevant CNV,
 51 | were generated for assembly GRCh37, one for copy_number_loss, and one for copy_number_gain.
 52 | 
 53 | 
 54 | | NR SV file | Records with clinical_significance |
 55 | |:--------------------------------------:|:----------------------------------:|
 56 | | GRCh37.copy_number_gain.with_SCV.bedpe | 13016 |
 57 | | GRCh37.copy_number_loss.with_SCV.bedpe | 10872 |
 58 | 
 59 | 
 60 | As an example of further processing of the output files, here is a table showing counts of
 61 | NR SV records with pathogenic clinical_signicance:
 62 | 
 63 | 
 64 | | Count | GRCh37 gains | GRCh37 losses |
 65 | |:---------------------:|:---------------------:|:---------------------:|
 66 | |records with Pathogenic only|1974|3939|
 67 | |records with Pathogenic and another clinical_significance|44|48|
 68 | |records with one or more Pathogenic|2018|3987|
 69 | | **Total records with clinical significance** | **13016** | **10872** |
 70 | 
 71 | 
 72 | 
 73 | ##### 1. Go to ftp site for deletions:
 74 | [https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/)
 75 | 
 76 | ##### 2. Download deletions bedpe file:
 77 | ###### GRCh37.nr_deletions.bedpe.gz
 78 | ##### 3. Get human clinically-relevant copy_number_loss records from deletions bedpe file:
 79 | ```markdown
 80 | zcat GRCh37.nr_deletions.bedpe.gz | grep SCV > GRCh37.copy_number_loss.with_SCV.bedpe
 81 | ```
 82 | ##### 4. Go to ftp site for duplications:
 83 | [https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications/](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications/)
 84 | ##### 5. Download duplications bedpe file:
 85 | ###### GRCh37.nr_duplications.bedpe.gz
 86 | 
 87 | ##### 6. Get human clinically-relevant copy_number_gain records from deletions bedpe file:
 88 | ```markdown
 89 | zcat GRCh37.nr_duplications.bedpe.gz | grep SCV > GRCh37.copy_number_gain.with_SCV.bedpe
 90 | ```
 91 | 
 92 | ##### 7. Link to dbVar web pages for additional variant details
 93 | 
 94 | Create URLs for dbVar variant pages using the nssv accessions in the bedpe files. For example:
 95 | 
 96 | [https://www.ncbi.nlm.nih.gov/dbvar/?term=nssv13649440](https://www.ncbi.nlm.nih.gov/dbvar/?term=nssv13649440)
 97 | 
 98 | From the latter page you may click on the "Variant Region ID" on the left to see the variant's region in the NCBI Variation Viewer at:
 99 | 
100 | [https://www.ncbi.nlm.nih.gov/dbvar/variants/nsv533950/](https://www.ncbi.nlm.nih.gov/dbvar/variants/nsv533950/)
101 | 
102 | ##### 8. Link to ClinVar web pages for additional clinical details
103 | 
104 | Use an SCV accession obtained from the bedpe files, e.g. SCV000045941, to find the corresponding record in ClinVar by searching for the SCV on ClinVar's home page:
105 | 
106 | [https://www.ncbi.nlm.nih.gov/clinvar/](https://www.ncbi.nlm.nih.gov/clinvar/)
107 | 
108 | 
109 | ----------
110 | 
111 | ### Find overlaps between NR-SV and candidate structural variants
112 | This case may be helpful if you would like to know if candidate structural variants compare to existing variants in dbVar.
113 | #### 1. Format your file or candidate structural variants as either gff, bed, or bedpe
114 | For example:
115 | variant_calls.gff:
116 | ```markdown
117 | chr13   dbVar   copy_number_gain        100217593       100233402       .       +       .       ID=chr13_100217593_100233402_copy_number_gain_1
118 | chr10   dbVar   copy_number_loss        78342182        78366362        .       +       .       ID=chr10_78342182_78366362_copy_number_loss_1
119 | chr5    dbVar   copy_number_loss        113158233       113172463       .       +       .       ID=ch
120 | ```
121 | #### 2. Download NR files
122 | Visit these directories to select the appropriate files according to assembly (GRCh37, GRCh38), or type (bed, bedpe):
123 | 
124 | [ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions](ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions)
125 | 
126 | [ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications](ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications)
127 | 
128 | [ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions](ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions)
129 | 
130 | NOTE: the .bedpe files have the most information about the variants, however, you can use .bedpe if you only care about the placements. Refer to https://github.com/ncbi/dbvar/tree/master/Structural_Variant_Sets/Nonredundant_Structural_Variants for list of columns included in the files.
131 | 
132 | For example, bedpe files on GRCh37:
133 | 
134 | [ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/GRCh37.nr_deletions.bedpe.gz](ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/GRCh37.nr_deletions.bedpe.gz)
135 | 
136 | [ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications/GRCh37.nr_duplications.bedpe.gz](ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications/GRCh37.nr_duplications.bedpe.gz)
137 | 
138 | [ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions/GRCh37.nr_insertions.bedpe.gz](ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions/GRCh37.nr_insertions.bedpe.gz)
139 | 
140 | 
141 | #### 3. NR files
142 | ```markdown
143 | gunzip GRCh37.nr_deletions.bedpe.gz
144 | gunzip GRCh37.nr_duplications.bedpe.gz
145 | gunzip GRCh37.nr_insertions.bedpe.gz
146 | ```
147 | #### 4. Run bedtools against each NR file
148 | For example, default to any overlap:
149 | ```markdown
150 | bedtools intersect -a variant_calls.gff -b GRCh37.nr_deletions.bedpe
151 | bedtools intersect -a variant_calls.gff -b GRCh37.nr_duplications.bedpe
152 | bedtools intersect -a variant_calls.gff -b GRCh37.nr_insertions.bedpe
153 | ```
154 | Example of narrower selection criteria, using at least 75% reciprocal overlap, and saving columns from both files to an output file:
155 | ```markdown
156 | bedtools intersect -a variant_calls.gff -b GRCh37.nr_deletions.bedpe -wo -r -f .75 > variant_calls_X_nr_deletions.gff
157 | bedtools intersect -a variant_calls.gff -b GRCh37.nr_duplications.bedpe -wo -r -f .75 > variant_calls_X_nr_duplications.gff
158 | bedtools intersect -a variant_calls.gff -b GRCh37.nr_insertions.bedpe -wo -r -f .75 > variant_calls_X_nr_insertions.gff
159 | ```
160 | #### 5. Interpret results:
161 | 
162 | For example, identify unique copy_number_loss variants with >75% reciprocal overlap with NR deletions:
163 | ```markdown
164 | cut -f 9 variant_calls_X_nr_deletions.gff | sort -u | grep loss | wc -l
165 | 675
166 | ```
167 | 
168 | Identify unique copy_number_gain variants with >75% reciprocal overlap with NR deletions:
169 | ```markdown
170 | cut -f 9 variant_calls_X_nr_duplications.gff | grep gain | sort -u | wc -l
171 | 558
172 | ```
173 | 
174 | Identify any variants with >75% reciprocal overlap to an NR variant with clinical significance of Pathogenic:
175 | ```markdown
176 | grep SCV variant_calls_X_nr_*.gff | grep Pathogenic
177 | chr16    dbVar   copy_number_loss        14945195    16363239 .       +       .       ID=chr16_14945195_16363239_copy_number_loss_1   chr16   14809981     16477578        .       -1      -1      chr16_14809981_16477578_del     .       .       .   copy_number_loss Oligo_aCGH      Probe_signal_intensity  NA      ClinGen_Laboratory-Submitted nssv585211;nssv3396567  Pathogenic      SCV000175002    large   .       .       1418045
178 | ```
179 | Using the -wo option to bedtools intersect returns the full set of columns from the NR bedpe file. You can use these columns to filter the results based on other criteria, such as method, platform, or study name. Refer to [https://github.com/ncbi/dbvar/tree/master/Structural_Variant_Sets/Nonredundant_Structural_Variants](https://github.com/ncbi/dbvar/tree/master/Structural_Variant_Sets/Nonredundant_Structural_Variants) for the list of columns included in the files.
180 | #### 6. Other options
181 | - Run bedtools with "-f 1" to find variants with 100% reciprocal overlap in NR.
182 | - Run bedtools with "-u" instead of "-wo" to see only unique id's from variant file.  For example:
183 | ```markdown
184 | bedtools intersect -a variant_calls.gff -b GRCh37.nr_deletions.bedpe -u -r -f 1 > variant_calls_X_nr_deletions.unique.100pct.gff
185 | more variant_calls_X_nr_deletions.unique.100pct.gff
186 | chr2    dbVar   copy_number_loss        165850456       165864123       .       +       .       ID=chr2_165850456_165864123_copy_number_loss_7
187 | 
188 | grep chr2_165850456_165864123_copy_number_loss_7 variant_calls_X_nr_deletions.gff
189 | ```
190 | 
191 | 
192 | ----------
193 | 
194 | ### Find overlaps between NR SVs and annotation datasets
195 | This case may be helpful if you would like to know if candidate structural variants overlap other NCBI annotation resources.
196 | 
197 | #### 1. Format your file or candidate structural variants as either gff, bed, or bedpe. For example:
198 | variant_calls.gff:
199 | 
200 | 
201 | ```
202 | chr12 dbVar short_tandem_repeat 132387673 132387821 . + . ID=chr12_132387673_132387821_short_tandem_repeat_1
203 | chr5 dbVar alu_insertion 62339523 62339830 . + . ID=chr5_62339523_62339830_alu_insertion_1
204 | chr9 dbVar insertion 137921881 137921881 . + . ID=chr9_137921881_137921881_insertion_7
205 | chr7 dbVar deletion 67715920 67716363 . + . ID=chr7_67715920_67716363_deletion_2
206 | ```
207 | 
208 | 
209 | 
210 | #### 2. Download and prepare annotation files
211 | GRCh37:
212 | Download the following:
213 | RefSeq annotations file, which include genes, exons, and regulatory regions: [ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz](ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz)
214 | 
215 | Paralogous alignments: [ftp://ftp.ncbi.nlm.nih.gov/pub/murphyte/PSV/GRCh37.p13_AR105/all.annot.gff3.gz](ftp://ftp.ncbi.nlm.nih.gov/pub/murphyte/PSV/GRCh37.p13_AR105/all.annot.gff3.gz)  
216 | 
217 | Dosage Sensitivity (more information here: [https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd45/](https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd45/)): [ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/gvf/nstd45.GRCh37.variant_region.gvf.gz](ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/gvf/nstd45.GRCh37.variant_region.gvf.gz)
218 | 
219 | Combine files and translate the NCBI accessions to chromosome names
220 | ```markdown
221 | gunzip ref_GRCh37.p13_top_level.gff3.gz all.annot.gff3.gz nstd45.GRCh37.variant_region.gvf.gz
222 | cat ref_GRCh37.p13_top_level.gff3 all.annot.gff3 nstd45.GRCh37.variant_region.gvf |
223 | grep -v "###" |  grep "^NC_" | sed "s/NC_000001.10/chr1/g" | sed "s/NC_000002.11/chr2/g" | sed "s/NC_000003.11/chr3/g" |
224 | sed "s/NC_000004.11/chr4/g" | sed "s/NC_000005.9/chr5/g" | sed "s/NC_000006.11/chr6/g" | sed "s/NC_000007.13/chr7/g" |
225 | sed "s/NC_000008.10/chr8/g" | sed "s/NC_000009.11/chr9/g" | sed "s/NC_000010.10/chr10/g" | sed "s/NC_000011.9/chr11/g" |
226 | sed "s/NC_000012.11/chr12/g" | sed "s/NC_000013.10/chr13/g" | sed "s/NC_000014.8/chr14/g" | sed "s/NC_000015.9/chr15/g" |
227 | sed "s/NC_000016.9/chr16/g" | sed "s/NC_000017.10/chr17/g" | sed "s/NC_000018.9/chr18/g" | sed "s/NC_000019.9/chr19/g" |
228 | sed "s/NC_000020.10/chr20/g" | sed "s/NC_000021.8/chr21/g" | sed "s/NC_000022.10/chr22/g" | sed "s/NC_000023.10/chrX/g" |
229 | sed "s/NC_000024.9/chrY/g" | sed "s/NC_012920.1/chrMT/g" | sort > annotations_37.gff
230 | ```
231 | 
232 | GRCh38:
233 | Download the following:
234 | 
235 | RefSeq annotations file, which include genes, exons, and regulatory regions: [ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz](ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz)
236 | 
237 | Assembly anomalies (more information here: [https://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/alignments](https://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/alignments)): [ftp://ftp.ncbi.nlm.nih.gov/pub/remap/Homo_sapiens/current/GCF_000001405.25_GRCh37.p13/GCF_000001405.38_GRCh38.p12/GCF_000001405.25-GCF_000001405.38.gff](ftp://ftp.ncbi.nlm.nih.gov/pub/remap/Homo_sapiens/current/GCF_000001405.25_GRCh37.p13/GCF_000001405.38_GRCh38.p12/GCF_000001405.25-GCF_000001405.38.gff)
238 | 
239 | Paralogous alignments: [ftp://ftp.ncbi.nlm.nih.gov/pub/murphyte/PSV/GRCh38.p2_AR107/GRCh38.p2_all.align.gff3.gz](ftp://ftp.ncbi.nlm.nih.gov/pub/murphyte/PSV/GRCh38.p2_AR107/GRCh38.p2_all.align.gff3.gz)
240 | 
241 | Dosage Sensitivity (more information here: [https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd45/](https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd45/)): [ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/gvf/nstd45.GRCh38.variant_region.gvf.gz](ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/gvf/nstd45.GRCh38.variant_region.gvf.gz)
242 | 
243 | Combine files and translate the NCBI accessions to chromosome names
244 | ```markdown
245 | gunzip ref_GRCh38.p12_top_level.gff3.gz GRCh38.p2_all.align.gff3.gz nstd45.GRCh38.variant_region.gvf.gz
246 | cat GCF_000001405.25-GCF_000001405.38.gff ref_GRCh38.p12_top_level.gff3  GRCh38.p2_all.align.gff3 nstd45.GRCh38.variant_region.gvf |
247 | grep -v "###" |  grep "^NC_" | sed "s/NC_000001.11/chr1/g" | sed "s/NC_000002.12/chr2/g" | sed "s/NC_000003.12/chr3/g" |
248 | sed "s/NC_000004.12/chr4/g" | sed "s/NC_000005.10/chr5/g" | sed "s/NC_000006.12/chr6/g" | sed "s/NC_000007.14/chr7/g" |
249 | sed "s/NC_000008.11/chr8/g" | sed "s/NC_000009.12/chr9/g" | sed "s/NC_000010.11/chr10/g" | sed "s/NC_000011.10/chr11/g" |
250 | sed "s/NC_000012.12/chr12/g" | sed "s/NC_000013.11/chr13/g" | sed "s/NC_000014.9/chr14/g" | sed "s/NC_000015.10/chr15/g" |
251 | sed "s/NC_000016.10/chr16/g" | sed "s/NC_000017.11/chr17/g" | sed "s/NC_000018.10/chr18/g" | sed "s/NC_000019.10/chr19/g" |
252 | sed "s/NC_000020.11/chr20/g" | sed "s/NC_000021.9/chr21/g" | sed "s/NC_000022.11/chr22/g" | sed "s/NC_000023.11/chrX/g" |
253 | sed "s/NC_000024.10/chrY/g" | sed "s/NC_012920.1/chrMT/g" | sort > annotations_38.gff
254 | ```
255 | 
256 | #### 3. Run bedtools
257 | This shows how you could identify the overlaps between your candidate structural variants and the downloaded annotation files.
258 | These examples identify overlaps with at least 75% reciprocal overlap, and the output files will contain columns from both the variant and annotation files.
259 | If your data is on GRCh37:
260 | ```markdown
261 | bedtools intersect -a variant_calls.gff -b annotations_37.gff  -wo -r -f .75 > variant_calls.gff_X_annotations_37.gff.min75
262 | ```
263 | If your data is on GRCh38:
264 | ```markdown
265 | bedtools intersect -a variant_calls.gff -b annotations_38.gff  -wo -r -f .75 > variant_calls.gff_X_annotations_38.gff.min75
266 | ```
267 | 
268 | #### 4. Interpret Results
269 | Identify unique variants with >75% reciprocal overlap with GRCh38 annotation files:
270 | ```markdown
271 | cut -f 9 variant_calls.gff_X_annotations_38.gff.min75 | sort -u| wc -l
272 | ```
273 | Examine the result file. The GFF files used for annotation will contain a rich set of descriptions in the attribute column, for example:
274 | ```markdown
275 | cut -f 18 variant_calls.gff_X_annotations_38.gff.min75 | more
276 | ID=rna15957;Parent=gene5140;Dbxref=GeneID:105373346,Genbank:XR_002959474.1;Name=XR_002959474.1;gbkey=
277 | ncRNA;gene=LOC105373346;model_evidence=Supporting evidence includes similarity to: 5 ESTs%2C 20 long
278 | SRA reads%2C and 99%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 4
279 | samples with support for all annotated introns;product=uncharacterized LOC105373346%2C transcript var
280 | iant X25;transcript_id=XR_002959474.1
281 | ```
282 | 
283 | NOTE: For intersections between GFF and GFF files, col 19 will contain the number of overlapping bases.
284 | 
285 | ----------
286 | 


--------------------------------------------------------------------------------
/Structural_Variant_Sets/Nonredundant_Structural_Variants/README.md:
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  1 | # dbVar Human Nonredundant Structural Variants (NR SVs)
  2 | 
  3 | ### Work in progress - data subject to change
  4 | 
  5 | Documentation updated:  04/23/2020
  6 | 
  7 | ## Data Summary
  8 | 
  9 | 
 10 | See also [https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/release_notes/NR_stats.latest.txt](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/release_notes/NR_stats.latest.txt#github)
 11 |  
 12 | FTP Directory: <a href="https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant">nonredundant</a><br />
 13 | Last modified: Jul 5, 2022<br />
 14 | File types: bed, bedpe, tsv<br />
 15 | <h3>
 16 | Deletions</h3>
 17 | <table>
 18 | <tbody>
 19 | <tr>
 20 | <th>Type and FTP Directory</th>
 21 | <th>GRCh37</th>
 22 | <th>GRCh38</th>
 23 | <tr>
 24 | <td>All</td>
 25 | <td>1,944,208</td>
 26 | <td>1,944,574</td>
 27 | </tr>
 28 | <tr>
 29 | <td>Common</td>
 30 | <td>211,888</td>
 31 | <td>211,465</td>
 32 | </tr>
 33 | <tr>
 34 | <td>Pathogenic</td>
 35 | <td>17,333</td>
 36 | <td>17,160</td>
 37 | </tr>
 38 | <tr>
 39 | <td>Somatic</td>
 40 | <td>23,365</td>
 41 | <td>23,324</td>
 42 | </tr>
 43 | <tr>
 44 | <td>All-ACMG</td>
 45 | <td>5,827</td>
 46 | <td>5,838</td>
 47 | </tr>
 48 | <tr>
 49 | <td>Common-ACMG</td>
 50 | <td>392</td>
 51 | <td>403</td>
 52 | </tr>
 53 | <tr>
 54 | <td>Pathogenic-ACMG</td>
 55 | <td>2,840</td>
 56 | <td>2,841</td>
 57 | </tr>
 58 | <tr>
 59 | <td>Somatic-ACMG</td>
 60 | <td>966</td>
 61 | <td>965</td>
 62 | </tr>
 63 | </tbody>
 64 | </table>
 65 | <h3>
 66 | Duplications</h3>
 67 | <table>
 68 | <tbody>
 69 | <tr>
 70 | <th>Type and FTP Directory</th>
 71 | <th>GRCh37</th>
 72 | <th>GRCh38</th>
 73 | <tr>
 74 | <td>All</td>
 75 | <td>658,229</td>
 76 | <td>659,117</td>
 77 | </tr>
 78 | <tr>
 79 | <td>Common</td>
 80 | <td>59,576</td>
 81 | <td>59,150</td>
 82 | </tr>
 83 | <tr>
 84 | <td>Pathogenic</td>
 85 | <td>4,655</td>
 86 | <td>4,531</td>
 87 | </tr>
 88 | <tr>
 89 | <td>Somatic</td>
 90 | <td>15,105</td>
 91 | <td>15,079</td>
 92 | </tr>
 93 | <tr>
 94 | <td>All-ACMG</td>
 95 | <td>4,608</td>
 96 | <td>4,682</td>
 97 | </tr>
 98 | <tr>
 99 | <td>Common-ACMG</td>
100 | <td>125</td>
101 | <td>129</td>
102 | </tr>
103 | <tr>
104 | <td>Pathogenic-ACMG</td>
105 | <td>903</td>
106 | <td>902</td>
107 | </tr>
108 | <tr>
109 | <td>Somatic-ACMG</td>
110 | <td>811</td>
111 | <td>810</td>
112 | </tr>
113 | </tbody>
114 | </table>
115 | <h3>
116 | Insertions</h3>
117 | <table>
118 | <tbody>
119 | <tr>
120 | <th>Type and FTP Directory</th>
121 | <th>GRCh37</th>
122 | <th>GRCh38</th>
123 | <tr>
124 | <td>All</td>
125 | <td>1,667,972</td>
126 | <td>1,678,782</td>
127 | </tr>
128 | <tr>
129 | <td>Common</td>
130 | <td>121,240</td>
131 | <td>121,187</td>
132 | </tr>
133 | <tr>
134 | <td>Pathogenic</td>
135 | <td>182</td>
136 | <td>182</td>
137 | </tr>
138 | <tr>
139 | <td>All-ACMG</td>
140 | <td>3,413</td>
141 | <td>3,489</td>
142 | </tr>
143 | <tr>
144 | <td>Common-ACMG</td>
145 | <td>255</td>
146 | <td>261</td>
147 | </tr>
148 | <tr>
149 | <td>Pathogenic-ACMG</td>
150 | <td>55</td>
151 | <td>55</td>
152 | </tr>
153 | </tbody>
154 | </table>
155 | 
156 | All files are available in **bed**, **bedpe**, and **tsv** formats:
157 | 
158 | [https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/#github)
159 | [https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions/](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions//#github)
160 | [https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications/](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications//#github)
161 | 
162 | 
163 | 
164 | ## Description of NR SV data files:
165 | 
166 | * Sets of "non-redundant structural variations" (NR SVs) derived from dbVar are
167 | available via FTP as tab delimited files by assembly, GRCh37 & GRCh38, and type of variant.  
168 | 
169 | * Non-redundant refers to variant coordinates, i.e. chr, outermost start, and
170 | outermost stop.  Please note: the non-redundant coordinates are based strictly
171 | on exact overlap of coordinates, not on partial overlaps.  
172 | 
173 | * Other features of NR SV files:
174 |    * variant calls are from germline samples only (no somatic)
175 |    * placements are "BestAvailable" on the assembly (guarantees no duplicate placements for a variant)
176 |    * placements are on finished chromosomes only (not on NT_ or NW_ contigs)
177 |    * placements are 1-based in the .tsv files
178 |    * placements are zero-based start and 1-based stop in .bed and .bedpe files
179 |    * insertion_length is set to sequence length if the sequence was submitted to dbVar without a specific insertion_length
180 |    * insertions submitted to dbVar without insertion_length or submitted sequence are not included in the NR files
181 | 
182 | * Other files based on NR SV files:
183 |    * NR SV files annotated with overlapping ACMG genes
184 |    * NR SV files in .bed format
185 |    * NR SV files in .bedpe format
186 | 
187 | 
188 | 
189 | 
190 | ## File format:
191 | 
192 | Column | NR SV TSV File | BED File | BEDPE File |
193 | -----|:---------|:---|:------
194 | |1|chr|chr|chr|
195 | |2|outermost_start (1-based)|outermost_start (0-based)|outermost_start (0-based)|
196 | |3|outermost_stop (1-based)|outermost_stop (1-based)|outermost_stop (1-based)|
197 | |4|variant_count|NR_SV_id|.  (chrom2)|
198 | |5|variant_type| |-1  (start2)|
199 | |6|method| |-1  (end2)|
200 | |7|analysis| |NR_SV_id|
201 | |8|platform| |.  (score)|
202 | |9|study| |.  (strand1)|
203 | |10|variant| |.  (stramd2)|
204 | |11|clinical_assertion| |variant_count|
205 | |12|clinvar_accession| |variant_type|
206 | |13|bin_size| |method|
207 | |14|min_insertion_length*| |analysis|
208 | |15|max_insertion_length*| |platform|
209 | |16| | |study|
210 | |17| | |variant|
211 | |18| | |clinical_assertion|
212 | |19| | |clinvar_accession|
213 | |20| | |bin_size|
214 | |21| | |min_insertion_length|
215 | |22| | |max_insertion_length|
216 | 
217 | Please note:
218 |  * \* = NR_SV TSV fields 14 and 15 are in nr_insertion.tsv files only
219 |  * NR_SV_id = chr_outermost_start_outermost_stop_type where type is del, dup, or ins
220 |  * bin_size = small (length < 50 bp), medium (< 1000000), large (>= 1000000).  Length = outermost_stop - outermost_start + 1. 
221 |  * In all cases, bedpe columns 4 through 6, and 8 through 10, are populated with default values per the bedpe specification
222 |  * The bed and bedpe specifications are found here: https://bedtools.readthedocs.io/en/latest/content/general-usage.html
223 | 
224 | 
225 | ## Some fields may have multiple values: 
226 | * The fields type, method, analysis, platform, variant, study, clinical_significance, clinvar_accession, and gene may contain multiple values.  
227 | * Each of the values is associated with one or more calls found in the variant field.  
228 | * The values in the variant field are "dbVar call accessions". 
229 | 
230 | # Records in the NR SV files:
231 | 
232 | ## Records in the deletions or duplications NR SV files, e.g.:  
233 | 
234 | | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clincical_assertion | clinvar_accession | bin_size | 
235 | ----|-----------------|----------------|---------------|--------------|--------|----------|----------|-------|-------------|-------------------|-------------------|---------|
236 | 15 | 98085101 | 101843270 | 1 | copy_number_loss | Oligo_aCGH | Probe_signal_intensity | Agilent ISCA 44K | ClinGen_Laboratory-Submitted | nssv14082018 | Pathogenic | SCV000586438
237 | 
238 | ## Records in the insertions NR SV files, e.g.:
239 | 
240 | | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clincical_assertion | clinvar_accession | bin_size | min_insertion_length | max_insertion_length |
241 | ----|-----------------|----------------|---------------|--------------|--------|----------|----------|-------|-------------|-------------------|---------|-------|----------|----------------------|
242 | 1 | 1889055 | 1889055 | 1 | alu_insertion | Sequencing | Split_read_and_paired-end_mapping | HiSeq 2000 | Gardner2017 | nssv14051747 |  |  | small | 258 | 258
243 | 
244 | * only insertion SVs have minimum_insertion_length and maximum_insertion_length fields
245 | 
246 | ## Records in the NR SV .bed files, e.g.
247 | 
248 | chr | outermost_start | outermost_stop | NR_SV_id  
249 | ----|-----------------|----------------|-----
250 | chr1 | 0 | 10000 | chr1_0_10000_del
251 | 
252 | * Placements in bed files are zero-based start and one-based stop
253 | * name is comprised of chromosome, outermost_start, outermost_stop, and type (del, dup, or ins)
254 | * NR SV .bed files may be used with a variety of tools as shown in the tutorial:
255 | 
256 | https://github.com/ncbi/dbvar/blob/master/Structural_Variant_Sets/Nonredundant_Structural_Variants/ToolGuide.md
257 | 
258 | 
259 | ## Records in the NR SV .bedpe files, e.g.
260 | 
261 | chr | outermost_start | outermost_stop | chrom2 | start2 | end2 | NR_SV_id | score | strand1 | strand2 | variant_count | variant_type | method | analysis | platform | study | variant | clinical_assertion | clinvar_accession
262 | -------|--------|------|--------|--------|------|------|-------|---------|---------|----------|--------------|--------|----------|----------|-------|----|--------------------|------------------
263 | chr1 | 14873 | 7527302 | . | -1 | -1 | chr1_14873_7527302_del | . | . | . | 1 | copy_number_loss | Oligo_aCGH | Probe_signal_intensity | NA | ClinGen_Laboratory-Submitted | nssv13638713 | Pathogenic | SCV000495999
264 | 
265 | * Placements in bedpe files are zero-based start and one-based stop
266 | * bedpe files are normally used for disjointed genomic sequences
267 | * the NR bedpe files do not contain disjointed genomic sequences, and instead use default values for chrom2, start2 and end2 
268 | * the NR bedpe files use the optional fields starting at field 11 to hold: chr, outermost_start, outermost_stop, name, and all the additional fields which are in the NR SV files  
269 | 
270 | # ACMG files as "proof of principle" for a "use case"
271 | 
272 | ## Records in the NR SV ACMG files contain a field for the ACMG gene that overlaps the variant, e.g.:
273 | 
274 | chr | outermost_start | outermost_stop | variant_count | variant_type | method | analysis | platform | study | variant | clinical_significance | clinvar_accession | bin_size | min_insertion_length | max_insertion_length | gene
275 | ----|-----------------|----------------|---------------|--------------|--------|----------|----------|-------|-------------|-------------------|-------------------|----------------------|----------------------|-----|-----
276 | 3| 30621876 | 30621876 | 2 | alu_insertion | Merging;Sequencing | Merging;Split_read_and_paired-end_mapping | See merged experiments;HiSeq 2000 | 1000_Genomes_Consortium_Phase_3_SV_Submission;Gardner2017 | essv18243203;nssv14059593 |  |  | small |279 | 280 | TGFBR2 
277 | 
278 | ### Caveats for the ACMG files:
279 | 
280 | * ACMG files are provided as a "proof of principle" for a "use case" for the NR SV files.
281 | * ACMG files are based on region/gene overlaps, and are missing a few call/gene overlaps in the cases where the parent variant region does not include all of the variant call placement and the region does not overlap the gene or is upstream or downstream of the gene.   
282 | * Placements in the ACMG files do not account for confidence intervals, even though the overlaps reported in the file were determined using confidence intervals. This results in a few of the overlaps that are not supported by the placements as reported in the file.
283 | 
284 | For information on ACMG genes please see:
285 | https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/
286 | 
287 | # Methods and Analyses 
288 | ## example values
289 | 
290 | | Methods include, e.g. | Analyses include, e.g. |
291 | |:--------------------:|:--------------------:|
292 | | BAC_aCGH | Curated |
293 | | Curated | Genotyping |
294 | | MLPA | Local_sequence_assembly |
295 | | Merging | Merging |
296 | | Multiple | Multiple |
297 | | Not_provided | Not_provided |
298 | | Oligo_aCGH | Optical_mapping |
299 | | Optical_mapping | Other |
300 | | ROMA | Paired-end_mapping |
301 | | SNP_array | Probe_signal_intensity |
302 | | Sequencing | Read_depth |
303 | | qPCR | SNP_genotyping_analysis |
304 | | ROMA | Sequence_alignment |
305 | | SNP_array | Split_read_mapping |
306 | | Sequencing | de_novo_sequence_assembly |
307 | 
308 | # README files for deletions, insertions, and duplications
309 | 
310 | Please see README files for deletions, insertions, and duplications for example
311 | records and additional details.
312 | 
313 | * Deletions: https://github.com/ncbi/dbvar/blob/master/Structural_Variant_Sets/Nonredundant_Structural_Variants/Deletions/README.md
314 | * Insertions: https://github.com/ncbi/dbvar/blob/master/Structural_Variant_Sets/Nonredundant_Structural_Variants/Insertions/README.md
315 | * Duplications:
316 | https://github.com/ncbi/dbvar/blob/master/Structural_Variant_Sets/Nonredundant_Structural_Variants/Duplications/README.md
317 | 
318 | # Brief Outline of algorithm used to generate NR-SVs.
319 | 
320 | The algorithm makes use of previously existing scripts.
321 | 
322 | Input files are generated from the dbVar database with tab separated values and
323 | contain SVs by assembly, type, and other relevant fields.
324 | 
325 | Selected type files are grouped into "aggregated type files" as specified above,
326 | by chr.
327 | 
328 | The "aggregated type files" are converted into XML records containing all the
329 | neccessary fields required by the nr process.
330 | 
331 | The XML is then parsed to generate SV records with coordinates, type,
332 | method, analysis, platform, insertion_length, SV accession and study.  
333 | 
334 | The SV records are then processed to generate NR SV tab-separated value (tsv) files by assembly and type, as described above, e.g. 
335 | * GRCh38.nr_deletions.tsv.gz
336 | 
337 | # Tutorials
338 | 
339 | Examples of using the NR files with various tools and browsers can be found in: https://github.com/ncbi/dbvar/blob/master/Structural_Variant_Sets/Nonredundant_Structural_Variants/ToolGuide.md
340 | 
341 | # Questions or feedback
342 | 
343 | * Please email dbvar@ncbi.nlm.nih.gov or create an issue on this GitHub page.
344 | 
345 | # Thanks!
346 | 
347 | Thanks for your interest in the dbVar human "non-redundant structural variations" (NR SVs)
348 | data files from NCBI.
349 | 
350 | Please check back soon for further updates.
351 | 


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  1 | # Tool Guide – How to Use dbVar's NR SV Data Files
  2 | ## Purpose
  3 | 
  4 | This tutorial demonstrates how to intersect dbVar's non-redundant (NR) files with other genomic interval files using popular tools and browsers. By the end of the tutorial you should be able toe, for example, calculate overlaps between genes and NR Deletions throughout the human genome.
  5 | 
  6 | ## Tools
  7 |  - [Input Files](#input-files)
  8 |  - [Bedtools](#bedtools)
  9 |  - [Galaxy](#galaxy)
 10 |  - [UCSC Genome Browser](#ucsc-genome-browser)
 11 |  - [NCBI Sequence Viewer](#ncbi-sequence-viewer)
 12 |  - [Installation Notes (Linux)](#installation-notes-linux)
 13 | 
 14 | ## Input Files
 15 | ### dbVar NR Files
 16 | NOTES:
 17 |  - Many genome browsers can access dbVar's NR data files directly using the URLs provided, avoiding the need to download.
 18 |  - Some locally-installed tools may require you to download data files before use.
 19 |  - BED files have 0-based starts and 1-based stops. (Standard non-BED dbVar files use 1-based starts.)
 20 |  - Chromosome names contain "chr", e.g., **chrX**.
 21 |  - Some scenarios may require you to edit data files after download, using any plain text editor. Instructions are provided (see ***Post-Download instructions*** below). For example, the UCSC Genome Browser requires BED files to include a track name and description, and the removal of any placements on chrMT (usually located at the end of a file).
 22 |  - All **FTP directory/ file** paths in the table below should be prefixed with: ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/...
 23 | 
 24 | |File Content|File format|FTP directory/ file|Post-Download instructions|
 25 | |------------|-----------|--------|--------------------------|
 26 | |non-redundant ***Deletions***|BED|...deletions/ GRCh38.nr_deletions.bed.gz|```gunzip GRCh38.nr_deletions.bed.gz; echo "track name=\"dbVar NR deletions\" description=\"non-redundant deletions from dbVar\"" > GRCh38.nr_deletions_ucsc.bed; grep -v ^chrMT GRCh38.nr_deletions.bed >> GRCh38.nr_deletions_ucsc.bed```|
 27 | |non-redundant ***Duplications***|BED|...duplications/ GRCh38.nr_duplications.bed.gz|```gunzip GRCh38.nr_duplications.bed.gz```|
 28 | |non-redundant ***Insertions***|BED|...insertions/ GRCh38.nr_insertions.bed.gz|```gunzip GRCh38.nr_insertions.bed.gz```|
 29 | 
 30 | 
 31 | ### Query Files
 32 | 
 33 | Download and run instructions to generate these modified files for testing intersections using locally-installed tools, such as **bedtools:**
 34 | 
 35 | NOTES:
 36 |  - FTP files are located at ftp://ftp.ncbi.nlm.nih.gov
 37 |  - clinvar_chr.vcf
 38 |    - "chr" in chromosome names for consistency with the .bed files
 39 | - genes_chr.gff
 40 |    - for simplicity, filter just the genes on finished chromosomes
 41 |    - convert chromosome accessions to names for consistency with the .bed files
 42 | 
 43 | **NOTE:** these types of modifications may not be necessary depending on the format of your specific input file.
 44 | 
 45 | |File Content|File format|FTP directory/ file|Modified File Name|Post-Download instructions|
 46 | |------------|-----------|-----------------|------------------|--------------------------|
 47 | |Clinical variants|.vcf|/pub/clinvar/vcf_GRCh38/ clinvar.vcf.gz|clinvar_chr.vcf|gunzip clinvar.vcf.gz; grep "^#" clinvar.vcf > clinvar_chr.vcf; grep -v "^#" clinvar.vcf \| sed "s/^/chr/" >> clinvar_chr.vcf|
 48 | |Human genes|.gff|/refseq/H_sapiens/H_sapiens/GFF/ ref_GRCh38.p12_top_level.gff3.gz|genes_chr.gff|gunzip ref_GRCh38.p12_top_level.gff3.gz;  grep "^#" ref_GRCh38.p12_top_level.gff3 > genes_chr.gff; cat ref_GRCh38.p12_top_level.gff3 \| awk -F'\t' '$3~/^gene$/' \| grep "^NC_" \| sed "s/NC_000001.11/chr1/g" \| sed "s/NC_000002.12/chr2/g" \| sed "s/NC_000003.12/chr3/g" \| sed "s/NC_000004.12/chr4/g" \| sed "s/NC_000005.10/chr5/g" \| sed "s/NC_000006.12/chr6/g" \| sed "s/NC_000007.14/chr7/g" \| sed "s/NC_000008.11/chr8/g" \| sed "s/NC_000009.12/chr9/g" \| sed "s/NC_000010.11/chr10/g" \| sed "s/NC_000011.10/chr11/g" \| sed "s/NC_000012.12/chr12/g" \| sed "s/NC_000013.11/chr13/g" \| sed "s/NC_000014.9/chr14/g" \| sed "s/NC_000015.10/chr15/g" \| sed "s/NC_000016.10/chr16/g" \| sed "s/NC_000017.11/chr17/g" \| sed "s/NC_000018.10/chr18/g" \| sed "s/NC_000019.10/chr19/g" \| sed "s/NC_000020.11/chr20/g" \| sed "s/NC_000021.9/chr21/g" \| sed "s/NC_000022.11/chr22/g" \| sed "s/NC_000023.11/chrX/g" \| sed "s/NC_000024.10/chrY/g" \| sed "s/NC_012920.1/chrMT/g" >> genes_chr.gff|
 49 | 
 50 | 
 51 | # Bedtools:
 52 | ### Compute Intersections
 53 | Refer to:
 54 |  - <http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html>
 55 |  - **Installation Notes** section at end of this document.
 56 | 
 57 | To find ClinVar variants that intersect dbVar deletions, run:
 58 | 
 59 |     `bedtools intersect -a clinvar_chr.vcf -b GRCh38.nr_deletions.bed -u > clinvar_dbvar_deletions.vcf`
 60 | 
 61 | To find genes that intersect dbVar insertions, run:
 62 | 
 63 |     `bedtools intersect -a genes_chr.gff -b GRCh38.nr_insertions.bed -u > gene_dbvar_insertions.gff`
 64 | 
 65 | *NOTE:*  The **-u** option provides a **unique** set of overlaps.
 66 | 
 67 | 
 68 | # Galaxy:
 69 | ### Compute Intersections
 70 |  - Go to the online Galaxy server: <https://usegalaxy.org/>
 71 |   - If the server is down, select an alternate server from the displayed list.
 72 |  - Select **Get Data** from the **Tools** menubar
 73 |  - Select **Upload File** from your computer under **Get Data**
 74 |  - In the **Download from web or upload from disk** window
 75 |    - select **Paste/Fetch data**
 76 |    - Paste the FTP URL in the text box, for example: <ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/GRCh38.nr_deletions.bed.gz>
 77 |    - Select **Start**
 78 |    - Wait for the file to complete loading
 79 |  - In the **Download from web or upload from disk** window
 80 |    - Select **Paste/Fetch data**
 81 |    - Paste the FTP URL in the text box, for example: <ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions/GRCh38.nr_insertions.bed.gz>
 82 |    - Select **Start**
 83 |    - Wait for the file to complete loading
 84 |    - Select **Close**
 85 |  - Both files should now be displayed in the **History** column
 86 |  - Select **Operate on Genomic Intervals** from the **Tools** menubar (you may need to scroll down)
 87 |  - Select **Intersect** under **Operate on Genomic Intervals**
 88 |  - In the **Intersect the intervals of two datasets (Galaxy Version 1.0.0)** window:
 89 |    - Select Downloaded file 1 as the First dataset
 90 |    - Select Downloaded file 2 as the Second dataset
 91 |    - Select **Execute**
 92 |  - Wait for the job to complete
 93 |  - When the job is complete, a new file will be displayed in the **History** column, named "**Intersect on data ... and data ...**"
 94 |  - Click the **Eye** icon on the new intersect results file to view the data
 95 |  - The intersection results will be displayed in the center column of page
 96 |  - For example:
 97 | ![Galaxy](../../images/galaxy.PNG?raw=true "Galaxy")
 98 | 
 99 | ### Compute Intersections (BED and VCF)
100 |  - Select **Get Data** from the **Tools** menubar
101 |  - Select **Upload File from your computer** under **Get Data**
102 |  - In the **Download from web or upload from disk** window
103 |    - Select **Choose local file**
104 |    - Navigate to the clinvar_chr.vcf file or any other local VCF file
105 |    - Select **Start**
106 |    - Wait for the file to complete loading
107 |    - Select **Close**
108 |  - Select **NGC VCF Manipulating** from the **Tools** menubar (you may need to scroll down)
109 |  - Select **VCF-BEDintersect**
110 |  - In the **VCF-BEDintersect: Intersect VCF and BED datasets (Galaxy Version 1.0.0)** window:
111 |    - Select VCF file, for example, clinvar_chr.vcf
112 |    - Select BED file, for example, downloaded GHRCh38.nr_deletions.bed.gz
113 |    - Select **Execute**
114 |  - Wait for the job to complete
115 |  - When the job is complete, a new file will be displayed in the **History** column, named **VCF-BEDintersect:on data ... and data ...**
116 |  - Click the **Eye** icon on the new intersect results file to view the data
117 |  - The intersection results will be displayed in the center column of page
118 |  - For example:
119 | ![Galaxy VCF](../../images/galaxy_vcf.PNG?raw=true "Galaxy")
120 | 
121 | 
122 | # UCSC Genome Browser:
123 | ### Browse
124 | 
125 |  - Open the **UCSC Genome Browser**: <http://genome.ucsc.edu/cgi-bin/hgGateway>
126 |  - Select **GRCh38/hg38** in the **Human Assembly** pull-down
127 |  - Select **Go**
128 |  - Select **Custom Tracks** from the **My Data** menu in the header menu
129 |  - In the **Paste URLs or data** entry form, select **Choose File**
130 |  - Navigate to select your bed file, for example, **GRCh38.nr_deletions_ucsc.bed**
131 |  - Select **Submit**
132 |  - NOTE: file requirements:
133 |    - "track" line containing name and description
134 |    - chr\* chromosome identifiers
135 |    - no chrMT
136 |    - Follow instructions in **Post-Download instructions** to generate valid file.
137 |  - The custom track name should be displayed in the **Manage Custom Tracks** page
138 |  - Select **Genome Browser** from the header menu
139 |  - The custom track should be displayed
140 |  - Right-click on the track to change the display from **dense** to **full**
141 |  - Zoom in or out sufficiently to see the individual variants
142 |  - Example of display:
143 | ![UCSC Genome Browser](../../images/ucsc_browser.PNG?raw=true "UCSC Genome Browser")
144 | 
145 | Add a second track of insertions:
146 |  - Select **Custom Tracks** from the **My Data** menu in the header menu
147 |  - In the **Paste URLs or data** text entry, paste the URL of the NR insertion file: <ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions/GRCh38.nr_insertions.bed.gz>
148 |  - NOTE:
149 |    - there are no chrMT in the insertion file
150 |    - load without a track name
151 |  - The new track should be displayed as "User Track" in the **Manage Custom Tracks** page
152 |  - Select **Genome Browser**  from the header menu
153 |  - Example of display:
154 | ![UCSC Genome Browser insertions](../../images/ucsc_browser_ins.PNG?raw=true "UCSC Genome Browser insertions")
155 | 
156 | ### Compute Intersections
157 |  - Select **Table Browser** from the **Tools** menu in the header menu.
158 |  - Select "Custom Tracks" from **group**, if not already displayed.
159 |  - Select the custom track name, for example, **dbVar NR deletions** from **track.**
160 |  - Select **create** next to **intersection.**
161 |  - The next window will be named: **Intersect with** *your track name*, for example: **Intersect with dbVar NR deletions.**
162 |  - Update the parameters, or use the defaults: **Genes and Gene Predictions.**
163 |  - Select **submit** from the **Intersect with ...** window.
164 |  - In the **Table Browser** window,:
165 |    - Select an **output format** or leave as **BED**
166 |    - Enter a name into **output file** (or leave blank to display output in browser)
167 |  - Select **get output**
168 |  - In the **Output ... as BED** window, select **getBED**
169 |  - The output is generated in a file or displayed in the browser.
170 | 
171 | 
172 | # NCBI Sequence Viewer:
173 | ### Browse
174 |  - Open **NCBI Sequence Viewer** for GRCh38, chromosome 1 in browser: <https://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000001>
175 |  - Select **Tracks**
176 |  - In **Configure Page** window, select **Custom Data**
177 |  - In **Data Source** menu, select **URL**
178 |  - In **URL** form, enter:
179 |    - **URL** <ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/GRCh38.nr_deletions.bed.gz>
180 |    - **Track Name**: dbVar NR deletions
181 |    - Select **Upload**
182 |  - In **URL** form, enter:
183 |    - **URL** <ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications/GRCh38.nr_duplications.bed.gz>
184 |    - **Track Name**: dbVar NR duplications
185 |    - Select **Upload**
186 |  - In **URL** form, enter:
187 |    - **URL** <ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions/GRCh38.nr_insertions.bed.gz>
188 |    - **Track Name**: dbVar NR insertions
189 |    - Select **Upload**
190 |  - In **URL** form:
191 |    - Select **Configure**
192 |  - All tracks should be displayed.
193 |    - Chromosome 1 top level:
194 | ![NCBI Sequence Browser chr1](../../images/NR_sv_chr1.PNG?raw=true "NCBI Sequence Browser chr1")
195 | 
196 |    - Chromosome 1 zoomed in:
197 | ![NCBI Sequence Browser zoom](../../images/NR_sv_chr1_zoom.PNG?raw=true "NCBI Sequence Browser zoomed")
198 | 
199 |    - Chromosome 1 showing detailed Non-redundant deletions, duplications, and insertions:
200 | ![NCBI Sequence Browser detail](../../images/NR_sv_chr1_detail.PNG?raw=true "NCBI Sequence Browser detail")
201 | 
202 | 
203 | # Installation Notes (Linux)
204 | ## Bedtools
205 |  - Find the latest bedtools directory in github, for example: <https://github.com/arq5x/bedtools2/releases/tag/v2.27.1>
206 |  - Download the \*.tar.gz file
207 |  - Go to the installation directory and run: `make`
208 |  - Add the bin directory to your path, for example:
209 |    `export PATH=/home/bedtools2.27/bin/:$PATH`
210 | 


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 1 | # dbVar Structural Variant (SV) Datasets
 2 | 
 3 | ## Work in progress, subject to change
 4 | 
 5 | Advances in genomic technologies have revealed structural variations (SV) to be prevalent in all human DNA, and subsequent research has increasingly implicated SV in phenotypic diversity and disease. In the next few years millions of genomes will be sequenced, leading to the discovery of many millions of SVs that will need to be analyzed to understand their functional impacts. A critical step in variant analysis and interpretation is the comparison of SVs found in an individual or population to known variants in public databases such as dbVar. Such comparisons can lead to biological insights into the possible functions of novel variants. To address the need for a SV reference, dbVar is creating structural variation datasets of known SV, complete with rich genomic and biological annotations, for use in novel SV analysis, annotaion, and related workflows.
 6 | 
 7 | dbVar is a NCBI database of human genomic structural variation with more than 5 million submitted SVs from 157 human studies. These include data from large diversity projects such as the 1000 Genomes Project and a global population CNV survey ([Sudmant et al. 2015](https://www.ncbi.nlm.nih.gov/pubmed/26249230)) and from clinical resources such as ClinVar and ClinGen. We utilized this large collection of variants to generate several non-redundant SV datasets, separated according to variant type. We have begun annotating these datasets using available information on genes, molecular consequence, clinical significance, dosage sensitivity, regulatory regions, and relevant genomic structural features such as repetitive regions, segmental duplications, and assembly-assembly alignment anomalous regions. These reference data and annotations are intended to facilitate the integration and comparison of dbVar SV data with other genome annotations (such as disease phenotype and population frequencies) and to provide insights into the impact of the SV on biological functions.
 8 | 
 9 | The resulting alpha-release datasets are currently available in tab-delimited formats at https://github.com/ncbi/dbvar/tree/master/Structural_Variant_Sets/Nonredundant_Structural_Variants. Our goal is to update these files on a regular basis incorporating new variant submissions, genomic features, Gene, RefSeq, ClinVar and other annotation information as it becomes available. We encourage users to test these files and to provide feedback, either by emailing dbvar@ncbi.nlm.nih.gov or by submitting a request directly at https://github.com/ncbi/dbvar/issues.
10 | 
11 | ============================
12 | 


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2 | 


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/images/ucsc_browser_ins.PNG:
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/nr_stats_tables/ftp_manifest-table4.20191104.inc.md:
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 1 | FTP Directory: <a href="ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant">nonredundant</a><br />
 2 | Last modified: Oct 22, 2019<br />
 3 | File types: bed, bedpe, tsv<br />
 4 | <h3>
 5 | Deletions</h3>
 6 | <table>
 7 |   <tbody>
 8 |     <tr>
 9 |     <th>Type and FTP Directory</th>
10 |     <th>GRCh37</th>
11 |     <th>GRCh38</th>
12 |     <tr>
13 |     <td>All</td>
14 |     <td>2,565,798</td>
15 |     <td>2,553,342</td>
16 |     </tr>
17 |     <tr>
18 |     <td>Common</td>
19 |     <td>256,543</td>
20 |     <td>255,992</td>
21 |     </tr>
22 |     <tr>
23 |     <td>Pathogenic</td>
24 |     <td>11,296</td>
25 |     <td>11,105</td>
26 |     </tr>
27 |     <tr>
28 |     <td>Somatic</td>
29 |     <td>23,360</td>
30 |     <td>23,319</td>
31 |     </tr>
32 |     </tbody>
33 |     </table>
34 |     <h3>
35 |     Duplications</h3>
36 |     <table>
37 |     <tbody>
38 |     <tr>
39 |     <th>Type and FTP Directory</th>
40 |     <th>GRCh37</th>
41 |     <th>GRCh38</th>
42 |     <tr>
43 |     <td>All</td>
44 |     <td>428,103</td>
45 |     <td>417,693</td>
46 |     </tr>
47 |     <tr>
48 |     <td>Common</td>
49 |     <td>68,992</td>
50 |     <td>68,447</td>
51 |     </tr>
52 |     <tr>
53 |     <td>Pathogenic</td>
54 |     <td>4,337</td>
55 |     <td>4,206</td>
56 |     </tr>
57 |     <tr>
58 |     <td>Somatic</td>
59 |     <td>15,103</td>
60 |     <td>15,077</td>
61 |     </tr>
62 |     </tbody>
63 |     </table>
64 |     <h3>
65 |     Insertions</h3>
66 |     <table>
67 |     <tbody>
68 |     <tr>
69 |     <th>Type and FTP Directory</th>
70 |     <th>GRCh37</th>
71 |     <th>GRCh38</th>
72 |     <tr>
73 |     <td>All</td>
74 |     <td>1,322,707</td>
75 |     <td>1,327,375</td>
76 |     </tr>
77 |     <tr>
78 |     <td>Common</td>
79 |     <td>138,871</td>
80 |     <td>138,737</td>
81 |     </tr>
82 |     <tr>
83 |     <td>Pathogenic</td>
84 |     <td>71</td>
85 |     <td>71</td>
86 |     </tr>
87 |     <tr>
88 |     <td>Somatic</td>
89 |     <td>0</td>
90 |     <td>0</td>
91 |     </tr>
92 |   </tbody>
93 | </table>
94 | 
95 | 


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/nr_stats_tables/test:
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  1 | <table>
  2 |   <thead>
  3 |     <tr>
  4 |       <th><h3>Supported Features</h3></th>
  5 |       <th width="40"><img src="https://raw.github.com/wiki/moxiecode/plupload/Required%20Features/html5.png" title="html5" /></th>
  6 |       <th colspan="2"><img src="https://raw.github.com/wiki/moxiecode/plupload/Required%20Features/flash.png" title="flash" /></th>
  7 |       <th colspan="2"><img src="https://raw.github.com/wiki/moxiecode/plupload/Required%20Features/silverlight.png" title="silverlight" /></th>
  8 |       <th width="40"><img src="https://raw.github.com/wiki/moxiecode/plupload/Required%20Features/html4.png" title="html4" /></th>
  9 |     </tr>
 10 |   </thead>
 11 |   <tbody>
 12 |     <tr>
 13 |       <th>Capability</th>
 14 |       <td width="40"><sup>browser</sup></td>
 15 |       <td width="40"><sup>browser</sup></td>
 16 |       <td width="40"><sup>client&nbsp;</sup></td>
 17 |       <td width="40"><sup>browser</sup></td>
 18 |       <td width="40"><sup> client </sup></td>
 19 |       <td width="40"><sup>browser</sup></td>
 20 |     </tr>
 21 |     <tr>
 22 |       <td>
 23 |         <strong>
 24 |           access_binary
 25 |         </strong> <br />
 26 |          <em style="font-size: 0.7em;">
 27 |         provide access to raw binary data of the file </em>
 28 |       </td>
 29 |       <td width="40"><span style="color: #006600;">✔</span></td>
 30 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_1">[1]</a></sup></td>
 31 |       <td width="40"><span style="color: red;">✘</span></td>
 32 |       <td width="40"><span style="color: #006600;">✔</span></td>
 33 |       <td width="40"><span style="color: #006600;">✔</span></td>
 34 |       <td width="40"><span style="color: #cc0000;">✘</span> <sup><a href="#wiki_fn_8">[8]</a></sup></td>
 35 |     </tr>
 36 |     <tr>
 37 |       <td>
 38 |         <strong>
 39 |           access&#95;image&#95;binary
 40 |         </strong><br />
 41 |         <em style="font-size: 0.7em;">
 42 |           provide access to raw binary data of the image
 43 |         </em>
 44 |       </td>
 45 |       <td width="40"><span style="color: #006600;">✔</span></td>
 46 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_1">[1]</a></sup></td>
 47 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
 48 |       <td width="40"><span style="color: #006600;">✔</span></td>
 49 |       <td width="40"><span style="color: #006600;">✔</span></td>
 50 |       <td width="40"><span style="color: #cc0000;">✘</span> <sup><a href="#wiki_fn_8">[8]</a></sup></td>
 51 |     </tr>
 52 |     <tr>
 53 |       <td>
 54 |         <strong>
 55 |           display_media
 56 |         </strong><br />
 57 |         <em style="font-size: 0.7em;">
 58 |         display binary data as thumbs for example </em>
 59 |       </td>
 60 |       <td width="40"><span style="color: #006600;">✔</span></td>
 61 |       <td width="40"><span style="color: #006600;">✔</span></td>
 62 |       <td width="40"><span style="color: #006600;">✔</span></td>
 63 |       <td width="40"><span style="color: #006600;">✔</span></td>
 64 |       <td width="40"><span style="color: #006600;">✔</span></td>
 65 |       <td width="40"><span style="color: #cc0000;">✘</span> <sup><a href="#wiki_fn_8">[8]</a></sup></td>
 66 |     </tr>
 67 |     <tr>
 68 |       <td>
 69 |         <strong>
 70 |           do_cors
 71 |         </strong><br />
 72 |         <em style="font-size: 0.7em;">
 73 |           make cross-domain requests
 74 |         </em>
 75 |       </td>
 76 |       <td width="40"><span style="color: #006600;">✔</span></td>
 77 |       <td width="40"><span style="color: #006600;">✔</span></td>
 78 |       <td width="40"><span style="color: #006600;">✔</span></td>
 79 |       <td width="40"><span style="color: #006600;">✔</span></td>
 80 |       <td width="40"><span style="color: #006600;">✔</span></td>
 81 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
 82 |     </tr>
 83 |     <tr>
 84 |       <td>
 85 |         <strong>
 86 |           drag&#95;and&#95;drop
 87 |         </strong><br />
 88 |         <em style="font-size: 0.7em;">
 89 |           accept files dragged and dropped from the desktop
 90 |         </em>
 91 |       </td>
 92 |       <td width="40"><span style="color: #006600;">✔</span></td>
 93 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
 94 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
 95 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
 96 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
 97 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
 98 |     </tr>
 99 |     <tr>
100 |       <td>
101 |         <strong>
102 |           filter&#95;by&#95;extension
103 |         </strong><br />
104 |         <em style="font-size: 0.7em;">
105 |           filter files in selection dialog by their extensions
106 |         </em>
107 |       </td>
108 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_7">[7]</a></sup></td>
109 |       <td width="40"><span style="color: #006600;">✔</span></td>
110 |       <td width="40"><span style="color: #006600;">✔</span></td>
111 |       <td width="40"><span style="color: #006600;">✔</span></td>
112 |       <td width="40"><span style="color: #006600;">✔</span></td>
113 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_7">[7]</a></sup></td>
114 |     </tr>
115 |     <tr>
116 |       <td>
117 |         <strong>
118 |           resize_image
119 |         </strong><br />
120 |         <em style="font-size: 0.7em;">
121 |           resize image
122 |         </em>
123 |       </td>
124 |       <td width="40"><span style="color: #006600;">✔</span></td>
125 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_1">[1]</a></sup></td>
126 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
127 |       <td width="40"><span style="color: #006600;">✔</span></td>
128 |       <td width="40"><span style="color: #006600;">✔</span></td>
129 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
130 |     </tr>
131 |     <tr>
132 |       <td>
133 |         <strong>
134 |           report&#95;upload&#95;progress
135 |         </strong><br />
136 |         <em style="font-size: 0.7em;">
137 |           periodically report how many bytes were uploaded
138 |         </em>
139 |       </td>
140 |       <td width="40"><span style="color: #006600;">✔</span></td>
141 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_2">[2]</a></sup></td>
142 |       <td width="40"><span style="color: #006600;">✔</span></td>
143 |       <td width="40"><span style="color: #006600;">✔</span></td>
144 |       <td width="40"><span style="color: #006600;">✔</span></td>
145 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
146 |     </tr>
147 |     <tr>
148 |       <td>
149 |         <strong>
150 |           return&#95;response&#95;headers
151 |         </strong><br />
152 |         <em style="font-size: 0.7em;">
153 |           provide access to the headers of http response
154 |         </em>
155 |       </td>
156 |       <td width="40"><span style="color: #006600;">✔</span></td>
157 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
158 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
159 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
160 |       <td width="40"><span style="color: #006600;">✔</span></td>
161 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
162 |     </tr>
163 |     <tr>
164 |       <td>
165 |         <strong>
166 |           return&#95;response&#95;type
167 |         </strong><br />
168 |         <em style="font-size: 0.7em;">
169 |         support http response of specific type </em>
170 |       </td>
171 |       <td width="40"><span style="color: #006600;">✔</span></td>
172 |       <td width="40"><span style="color: #006600;">✔</span></td>
173 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_9">[9]</a></sup></td>
174 |       <td width="40"><span style="color: #006600;">✔</span></td>
175 |       <td width="40"><span style="color: #006600;">✔</span></td>
176 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_9">[9]</a></sup></td>
177 |     </tr>
178 |     <tr>
179 |       <td>
180 |         <strong>
181 |           return&#95;status&#95;code
182 |         </strong><br />
183 |         <em style="font-size: 0.7em;">
184 |         return http status code of the response </em>
185 |       </td>
186 |       <td width="40"><span style="color: #006600;">✔</span></td>
187 |       <td width="40"><span style="color: #006600;">✔</span></td>
188 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_10">[10]</a></sup></td>
189 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_10">[10]</a></sup></td>
190 |       <td width="40"><span style="color: #006600;">✔</span></td>
191 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_10">[10]</a></sup></td>
192 |     </tr>
193 |     <tr>
194 |       <td>
195 |         <strong>
196 |           send&#95;custom&#95;headers
197 |         </strong> <br />
198 |         <em style="font-size: 0.7em;">
199 |           send custom http header with the request
200 |         </em>
201 |       </td>
202 |       <td width="40"><span style="color: #006600;">✔</span></td>
203 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_12">[12]</a></sup></td>
204 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
205 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
206 |       <td width="40"><span style="color: #006600;">✔</span></td>
207 |       <td width="40"><span style="color: #006600;">✔</span></td>
208 |     </tr>
209 |     <tr>
210 |       <td>
211 |         <strong>
212 |           select_file
213 |         </strong><br />
214 |         <em style="font-size: 0.7em;">
215 |           pick up a files from a dialog
216 |         </em>
217 |       </td>
218 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_3">[3]</a></sup></td>
219 |       <td width="40"><span style="color: #006600;">✔</span></td>
220 |       <td width="40"><span style="color: #006600;">✔</span></td>
221 |       <td width="40"><span style="color: #006600;">✔</span></td>
222 |       <td width="40"><span style="color: #006600;">✔</span></td>
223 |       <td width="40"><span style="color: #006600;">✔</span></td>
224 |     </tr>
225 |     <tr>
226 |       <td>
227 |         <strong>
228 |           select_folder
229 |         </strong><br />
230 |         <em style="font-size: 0.7em;">
231 |           select a folder from a dialog
232 |         </em>
233 |       </td>
234 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_3">[4]</a></sup></td>
235 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
236 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
237 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
238 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
239 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
240 |     </tr>
241 |     <tr>
242 |       <td>
243 |         <strong>
244 |           select_multiple
245 |         </strong><br />
246 |         <em style="font-size: 0.7em;">
247 |         select multiple files at once from a file dialog </em>
248 |       </td>
249 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_4">[5]</a></sup></td>
250 |       <td width="40"><span style="color: #006600;">✔</span></td>
251 |       <td width="40"><span style="color: #006600;">✔</span></td>
252 |       <td width="40"><span style="color: #006600;">✔</span></td>
253 |       <td width="40"><span style="color: #006600;">✔</span></td>
254 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
255 |     </tr>
256 |     <tr>
257 |       <td>
258 |         <strong>
259 |           send&#95;binary&#95;string
260 |         </strong><br />
261 |         <em style="font-size: 0.7em;">
262 |           send raw binary data (typically a binary string)
263 |         </em>
264 |       </td>
265 |       <td width="40"><span style="color: #006600;">✔</span></td>
266 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_1">[1]</a></sup></td>
267 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
268 |       <td width="40"><span style="color: #006600;">✔</span></td>
269 |       <td width="40"><span style="color: #006600;">✔</span></td>
270 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
271 |     </tr>
272 |     <tr>
273 |       <td>
274 |         <strong>
275 |           send&#95;browser&#95;cookies
276 |         </strong><br />
277 |         <em style="font-size: 0.7em;">
278 |         send browser cookies with http request </em>
279 |       </td>
280 |       <td width="40"><span style="color: #006600;">✔</span></td>
281 |       <td width="40"><span style="color: #006600;">✔</span></td>
282 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
283 |       <td width="40"><span style="color: #006600;">✔</span></td>
284 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
285 |       <td width="40"><span style="color: #006600;">✔</span></td>
286 |     </tr>
287 |     <tr>
288 |       <td>
289 |         <strong>
290 |           send_multipart
291 |         </strong> <br />
292 |         <em style="font-size: 0.7em;">
293 |           send multipart/form-data
294 |         </em>
295 |       </td>
296 |       <td width="40"><span style="color: #006600;">✔</span></td>
297 |       <td width="40"><span style="color: #006600;">✔</span></td>
298 |       <td width="40"><span style="color: #006600;">✔</span></td>
299 |       <td width="40"><span style="color: #006600;">✔</span></td>
300 |       <td width="40"><span style="color: #006600;">✔</span></td>
301 |       <td width="40"><span style="color: #006600;">✔</span></td>
302 |     </tr>
303 |     <tr>
304 |       <td>
305 |         <strong>
306 |           slice_blob
307 |         </strong><br />
308 |         <em style="font-size: 0.7em;">
309 |         slice the file or blob </em>
310 |       </td>
311 |       <td width="40"><span style="color: #006600;">✔</span></td>
312 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_1">[1]</a></sup></td>
313 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
314 |       <td width="40"><span style="color: #006600;">✔</span></td>
315 |       <td width="40"><span style="color: #006600;">✔</span></td>
316 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
317 |     </tr>
318 |     <tr>
319 |       <td>
320 |         <strong>
321 |           stream_upload
322 |         </strong><br />
323 |         <em style="font-size: 0.7em;">
324 |         upload file without preloading it to memory </em>
325 |       </td>
326 |       <td width="40"><span style="color: #006600;">✔</span></td>
327 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
328 |       <td width="40"><span style="color: #006600;">✔</span></td>
329 |       <td width="40"><span style="color: #006600;">✔</span></td>
330 |       <td width="40"><span style="color: #006600;">✔</span></td>
331 |       <td width="40"><span style="color: #006600;">✔</span></td>
332 |     </tr>
333 |     <tr>
334 |       <td>
335 |         <strong>
336 |           summon&#95;file&#95;dialog
337 |         </strong> <br />
338 |         <em style="font-size: 0.7em;">
339 |         programmatically trigger file dialog </em>
340 |       </td>
341 |       <td width="40"><span style="color: #006600;">✔</span></td>
342 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
343 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
344 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
345 |       <td width="40"><span style="color: #cc0000;">✘</span></td>
346 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_6">[6]</a></sup></td>
347 |     </tr>
348 |     <tr>
349 |       <td>
350 |         <strong>
351 |           upload_filesize
352 |         </strong><br />
353 |         <em style="font-size: 0.7em;">upload file of specific size </em>
354 |       </td>
355 |       <td width="40"><span style="color: #006600;">✔</span></td>
356 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_1">[1]</a></sup></td>
357 |       <td width="40"><span style="color: #006600;">✔</span></td>
358 |       <td width="40"><span style="color: #006600;">✔</span></td>
359 |       <td width="40"><span style="color: #006600;">✔</span></td>
360 |       <td width="40"><span style="color: #006600;">✔</span></td>
361 |     </tr>
362 |       <tr>
363 |       <td>
364 |         <strong>use&#95;http&#95;method
365 |         </strong><br />
366 |         <em style="font-size: 0.7em;">use specific http method</em></td>
367 |       <td width="40"><span style="color: #006600;">✔</span></td>
368 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_11">[11]</a></sup></td>
369 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_11">[11]</a></sup></td>
370 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_11">[11]</a></sup></td>
371 |       <td width="40"><span style="color: #006600;">✔</span></td>
372 |       <td width="40"><span style="color: #006600;">✔</span> <sup><a href="#wiki_fn_11">[11]</a></sup></td>
373 |     </tr>
374 |   </tbody>
375 | </table>
376 | 


--------------------------------------------------------------------------------
/specs/README.md:
--------------------------------------------------------------------------------
 1 | # dbVar Design and Schema Specifications
 2 | ============================
 3 | 
 4 | ### directory layout
 5 | 
 6 |     .
 7 |     +-- README.md
 8 |     +-- dbVar.xsd                             # dbVar database schema
 9 |     +-- dbVarSubmissionTemplate_v3.5.xlsx     # dbVar Submission Template (Excel)    
10 | 


--------------------------------------------------------------------------------
/specs/dbVar.xsd:
--------------------------------------------------------------------------------
   1 | <?xml version="1.0" encoding="UTF-8"?>
   2 | 
   3 | <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
   4 | 
   5 |     <xs:simpleType name="positive-decimal">
   6 |         <xs:annotation>
   7 |             <xs:documentation>The positive-decimal type specifies a positive decimal value.</xs:documentation>
   8 |         </xs:annotation>
   9 |         <xs:restriction base="xs:decimal">
  10 |             <xs:minExclusive value="0"/>
  11 |         </xs:restriction>
  12 |     </xs:simpleType>
  13 |     <xs:simpleType name="AlignmentCV">
  14 |         <xs:restriction base="xs:string">
  15 |             <xs:enumeration value="First Pass"/>
  16 |             <xs:enumeration value="Second Pass"/>
  17 |         </xs:restriction>
  18 |     </xs:simpleType>
  19 |     <xs:simpleType name="AnalysisTypeCV">
  20 |         <xs:annotation>
  21 |             <xs:documentation>
  22 |                 Controlled vocabulary for Analysis Type
  23 |             </xs:documentation>
  24 |         </xs:annotation>
  25 |         <xs:restriction base="xs:string">
  26 |             <xs:enumeration value="BAC assembly"/>
  27 |             <xs:enumeration value="Curated"/>
  28 |             <xs:enumeration value="de novo and local sequence assembly"/>
  29 |             <xs:enumeration value="de novo sequence assembly"/>
  30 |             <xs:enumeration value="Genotyping"/>
  31 |             <xs:enumeration value="Local sequence assembly"/>
  32 |             <xs:enumeration value="Manual observation"/>
  33 |             <xs:enumeration value="MCD analysis"/>
  34 |             <xs:enumeration value="Merging"/>
  35 |             <xs:enumeration value="Multiple"/>
  36 |             <xs:enumeration value="Not provided"/>
  37 |             <xs:enumeration value="One end anchored assembly"/>
  38 |             <xs:enumeration value="Optical mapping"/>
  39 |             <xs:enumeration value="Other"/>
  40 |             <xs:enumeration value="Paired-end mapping"/>
  41 |             <xs:enumeration value="Probe signal intensity"/>
  42 |             <xs:enumeration value="Read depth"/>
  43 |             <xs:enumeration value="Read depth and paired-end mapping"/>
  44 |             <xs:enumeration value="Sequence alignment"/>
  45 |             <xs:enumeration value="SNP genotyping analysis"/>
  46 |             <xs:enumeration value="Split read and paired-end mapping"/>
  47 |             <xs:enumeration value="Split read mapping"/>
  48 |         </xs:restriction>
  49 |     </xs:simpleType>
  50 |     <xs:simpleType name="BreakpointPairCV">
  51 |         <xs:annotation>
  52 |             <xs:documentation>
  53 |                 Controlled vocabulary to identify if this is From or To in a breakpoint pair               
  54 |             </xs:documentation>
  55 |         </xs:annotation>
  56 |         <xs:restriction base="xs:string">
  57 |             <xs:enumeration value="From"/>
  58 |             <xs:enumeration value="To"/>
  59 |         </xs:restriction>
  60 |     </xs:simpleType>
  61 |     <xs:simpleType name="CollectionCV">
  62 |         <xs:annotation>
  63 |             <xs:documentation>
  64 |                 Controlled vocabulary for subject collection              
  65 |             </xs:documentation>
  66 |         </xs:annotation>
  67 |         <xs:restriction base="xs:string">
  68 |             <xs:enumeration value="1000 Genomes">
  69 |                 <xs:annotation>
  70 |                     <xs:documentation>
  71 |                         Individual included in 1000 Genomes                
  72 |                     </xs:documentation>
  73 |                 </xs:annotation>
  74 |             </xs:enumeration>
  75 |             <xs:enumeration value="Autism"> </xs:enumeration>
  76 |             <xs:enumeration value="CEPH">
  77 |                 <xs:annotation>
  78 |                     <xs:documentation>
  79 |                         Individual included in CEPH panel                
  80 |                     </xs:documentation>
  81 |                 </xs:annotation>
  82 |             </xs:enumeration>
  83 |             <xs:enumeration value="HapMap">
  84 |                 <xs:annotation>
  85 |                     <xs:documentation>
  86 |                         Individual included in International HapMap Project               
  87 |                     </xs:documentation>
  88 |                 </xs:annotation>
  89 |             </xs:enumeration>
  90 |             <xs:enumeration value="HGDP">
  91 |                 <xs:annotation>
  92 |                     <xs:documentation>
  93 |                         Individual included in Human Genome Diversity Project                
  94 |                     </xs:documentation>
  95 |                 </xs:annotation>
  96 |             </xs:enumeration>
  97 |             <xs:enumeration value="NINDS">
  98 |                 <xs:annotation>
  99 |                     <xs:documentation>
 100 |                         Individual included in National Institute of Neurological Disorders and Stroke repository
 101 |                     </xs:documentation>
 102 |                 </xs:annotation>
 103 |             </xs:enumeration>
 104 |             <xs:enumeration value="OPGP">
 105 |                 <xs:annotation>
 106 |                     <xs:documentation>
 107 |                         Individual included in Ontario Population Genomics Platform
 108 |                     </xs:documentation>
 109 |                 </xs:annotation>
 110 |             </xs:enumeration>
 111 |             <xs:enumeration value="PDR">
 112 |                 <xs:annotation>
 113 |                     <xs:documentation>
 114 |                         Individual included in Polymorphism Discovery Resource                
 115 |                     </xs:documentation>
 116 |                 </xs:annotation>
 117 |             </xs:enumeration>
 118 |         </xs:restriction>
 119 |     </xs:simpleType>
 120 |     <xs:simpleType name="ContactRoleCV">
 121 |         <xs:annotation>
 122 |             <xs:documentation>
 123 |                 Controlled vocabulary for contact type    
 124 |             </xs:documentation>
 125 |         </xs:annotation>
 126 |         <xs:restriction base="xs:string">
 127 |             <xs:enumeration value="Submitter"/>
 128 |             <xs:enumeration value="First author"/>
 129 |             <xs:enumeration value="Senior author"/>
 130 |             <xs:enumeration value="Curator"/>
 131 |             <xs:enumeration value="Other"/>
 132 |         </xs:restriction>
 133 |     </xs:simpleType>
 134 |     <xs:simpleType name="ExperimentTypeCV">
 135 |         <xs:annotation>
 136 |             <xs:documentation>
 137 |                 Controlled vocabulary for Experiment Type    
 138 |             </xs:documentation>
 139 |         </xs:annotation>
 140 |         <xs:restriction base="xs:string">
 141 |             <xs:enumeration value="Discovery">
 142 |                 <xs:annotation>
 143 |                     <xs:documentation>
 144 |                         Experiment was used to discover structural variants               
 145 |                     </xs:documentation>
 146 |                 </xs:annotation>
 147 |             </xs:enumeration>
 148 |             <xs:enumeration value="Validation">
 149 |                 <xs:annotation>
 150 |                     <xs:documentation>
 151 |                         Experiment was used to validate structural variants                
 152 |                     </xs:documentation>
 153 |                 </xs:annotation>
 154 |             </xs:enumeration>
 155 |             <xs:enumeration value="Genotyping"/>
 156 |         </xs:restriction>
 157 |     </xs:simpleType>
 158 |     <xs:simpleType name="GenomicPlacementMethodCV">
 159 |         <xs:annotation>
 160 |             <xs:documentation>
 161 |                 Controlled vocabulary for genomic placement methods, default is genomic placements received from submitter.
 162 |             </xs:documentation>
 163 |         </xs:annotation>
 164 |         <xs:restriction base="xs:string">
 165 |             <xs:enumeration value="Remapped">
 166 |                 <xs:annotation>
 167 |                     <xs:documentation>
 168 |                         Original placement was mapped to another assembly using NCBI assembly-to-assembly remapping software. 
 169 |                     </xs:documentation>
 170 |                 </xs:annotation>
 171 |             </xs:enumeration>
 172 |             <xs:enumeration value="Remapped ad-hoc">
 173 |                 <xs:annotation>
 174 |                     <xs:documentation>
 175 |                         Original placement was mapped to another assembly by ad-hoc method at NCBI.
 176 |                     </xs:documentation>
 177 |                 </xs:annotation>
 178 |             </xs:enumeration>
 179 |             <xs:enumeration value="Submitted artifact">
 180 |                 <xs:annotation>
 181 |                     <xs:documentation>
 182 |                         Original placement was on an unplaced contig which is an artifact of the assembly.
 183 |                     </xs:documentation>
 184 |                 </xs:annotation>
 185 |             </xs:enumeration>
 186 |             <xs:enumeration value="Submitted cytogenetic">
 187 |                 <xs:annotation>
 188 |                     <xs:documentation>
 189 |                         Variant location was identified by cytoband, which were placed on genome by NCBI. 
 190 |                     </xs:documentation>
 191 |                 </xs:annotation>
 192 |             </xs:enumeration>
 193 |             <xs:enumeration value="Submitted genomic">
 194 |                 <xs:annotation>
 195 |                     <xs:documentation>
 196 |                         Original genomic placement provided by submitter.
 197 |                     </xs:documentation>
 198 |                 </xs:annotation>
 199 |             </xs:enumeration>
 200 |             <xs:enumeration value="Submitted HGVS">
 201 |                 <xs:annotation>
 202 |                     <xs:documentation>
 203 |                         Variant location was identified by HGVS nomenclature, in the hgvs_name field.
 204 |                     </xs:documentation>
 205 |                 </xs:annotation>
 206 |             </xs:enumeration>
 207 |             <xs:enumeration value="Remap failed">
 208 |                 <xs:annotation>
 209 |                     <xs:documentation>
 210 |                         Original placement did not successfully remap to specified assembly.
 211 |                     </xs:documentation>
 212 |                 </xs:annotation>
 213 |             </xs:enumeration>
 214 |             <xs:enumeration value="Submitted without placement on assembly">
 215 |                 <xs:annotation>
 216 |                     <xs:documentation>
 217 |                         Variant could not be placed on submitted assembly.
 218 |                     </xs:documentation>
 219 |                 </xs:annotation>
 220 |             </xs:enumeration>
 221 |             <xs:enumeration value="Submitted on non-INSDC assembly">
 222 |                 <xs:annotation>
 223 |                     <xs:documentation>
 224 |                         Submitted placement is on an assembly that is not in INSDC. Placements cannot be validated or loaded.
 225 |                     </xs:documentation>
 226 |                 </xs:annotation>
 227 |             </xs:enumeration>
 228 |         </xs:restriction>
 229 |     </xs:simpleType>
 230 |     <xs:simpleType name="LinkDbCV">
 231 |         <xs:annotation>
 232 |             <xs:documentation>
 233 |                 Controlled vocabulary for database Link, for an archive, phenotype, or sample resource                
 234 |             </xs:documentation>
 235 |         </xs:annotation>
 236 |         <xs:restriction base="xs:string">
 237 |             <xs:enumeration value="AE"/>
 238 |             <xs:enumeration value="BT"/>
 239 |             <xs:enumeration value="BioProj"/>
 240 |             <xs:enumeration value="BioSD"/>
 241 |             <xs:enumeration value="ClinGen"/>
 242 |             <xs:enumeration value="ClinVar"/>
 243 |             <xs:enumeration value="CLONE"/>
 244 |             <xs:enumeration value="CORIELL"/>
 245 |             <xs:enumeration value="COSMIC"/>
 246 |             <xs:enumeration value="dbGaP"/>
 247 |             <xs:enumeration value="dbSNP"/>
 248 |             <xs:enumeration value="dbSNP-batch"/>
 249 |             <xs:enumeration value="dbVar"/>
 250 |             <xs:enumeration value="DDBJ"/>
 251 |             <xs:enumeration value="DGV"/>
 252 |             <xs:enumeration value="DO"/>
 253 |             <xs:enumeration value="EGA"/>
 254 |             <xs:enumeration value="ENA"/>
 255 |             <xs:enumeration value="GEA"/>
 256 |             <xs:enumeration value="GENBANK"/>
 257 |             <xs:enumeration value="GENE"/>
 258 |             <xs:enumeration value="GeneReviews"/>
 259 |             <xs:enumeration value="GEO"/>
 260 |             <xs:enumeration value="HP"/>
 261 |             <xs:enumeration value="JAX"/>
 262 |             <xs:enumeration value="JGA"/>
 263 |             <xs:enumeration value="MedGen"/>
 264 |             <xs:enumeration value="MeSH"/>
 265 |             <xs:enumeration value="MONDO"/>
 266 |             <xs:enumeration value="OMIM"/>
 267 |             <xs:enumeration value="Orphanet"/>
 268 |             <xs:enumeration value="PROBE"/>
 269 |             <xs:enumeration value="PubMed"/>
 270 |             <xs:enumeration value="SRA"/>
 271 |             <xs:enumeration value="TRACE"/>
 272 |             <xs:enumeration value="UMLS"/>
 273 |         </xs:restriction>
 274 |     </xs:simpleType>
 275 |     <xs:simpleType name="MethodTypeCV">
 276 |         <xs:annotation>
 277 |             <xs:documentation>
 278 |                 Controlled vocabulary for Method Type
 279 |             </xs:documentation>
 280 |         </xs:annotation>
 281 |         <xs:restriction base="xs:string">
 282 |             <xs:enumeration value="BAC aCGH"/>
 283 |             <xs:enumeration value="Curated"/>
 284 |             <xs:enumeration value="Digital array"/>
 285 |             <xs:enumeration value="ddPCR"/>
 286 |             <xs:enumeration value="FISH"/>
 287 |             <xs:enumeration value="Gene expression array"/>
 288 |             <xs:enumeration value="Karyotyping"/>
 289 |             <xs:enumeration value="MAPH"/>
 290 |             <xs:enumeration value="MassSpec"/>
 291 |             <xs:enumeration value="Merging"/>
 292 |             <xs:enumeration value="Microsatellite genotyping"/>
 293 |             <xs:enumeration value="MLPA"/>
 294 |             <xs:enumeration value="Multiple complete digestion"/>
 295 |             <xs:enumeration value="Multiple"/>
 296 |             <xs:enumeration value="Not provided"/>
 297 |             <xs:enumeration value="Oligo aCGH"/>
 298 |             <xs:enumeration value="Optical mapping"/>
 299 |             <xs:enumeration value="PCR"/>
 300 |             <xs:enumeration value="qPCR"/>
 301 |             <xs:enumeration value="ROMA"/>
 302 |             <xs:enumeration value="RT-PCR"/>
 303 |             <xs:enumeration value="Sequencing"/>
 304 |             <xs:enumeration value="SNP array"/>
 305 |             <xs:enumeration value="Southern"/>
 306 |             <xs:enumeration value="Western"/>
 307 |         </xs:restriction>
 308 |     </xs:simpleType>
 309 |     <xs:simpleType name="OriginCV">
 310 |         <xs:annotation>
 311 |             <xs:documentation>
 312 |                 Controlled vocabulary for Variant_call Origin                  
 313 |             </xs:documentation>
 314 |         </xs:annotation>
 315 |         <xs:restriction base="xs:string">
 316 |             <xs:enumeration value="biparental"/>
 317 |             <xs:enumeration value="de novo"/>
 318 |             <xs:enumeration value="germline"/>
 319 |             <xs:enumeration value="Germline"/>
 320 |             <xs:enumeration value="inherited"/>
 321 |             <xs:enumeration value="maternal"/>
 322 |             <xs:enumeration value="Maternal"/>
 323 |             <xs:enumeration value="not applicable"/>
 324 |             <xs:enumeration value="not provided"/>
 325 |             <xs:enumeration value="not-reported"/>
 326 |             <xs:enumeration value="Not tested"/>
 327 |             <xs:enumeration value="paternal"/>
 328 |             <xs:enumeration value="Paternal"/>
 329 |             <xs:enumeration value="Present in both parents"/>
 330 |             <xs:enumeration value="see ClinVar for details"/>
 331 |             <xs:enumeration value="somatic"/>
 332 |             <xs:enumeration value="Somatic"/>
 333 |             <xs:enumeration value="tested-inconclusive"/>
 334 |             <xs:enumeration value="Tested - inconclusive"/>
 335 |             <xs:enumeration value="uniparental"/>
 336 |             <xs:enumeration value="unknown"/>
 337 |         </xs:restriction>
 338 |     </xs:simpleType>
 339 |     <xs:complexType name="PhenotypeLink">
 340 |         <xs:complexContent>
 341 |             <xs:extension base="LinkType">
 342 |                 <xs:attribute name="medgen_id" type="xs:string" use="optional"/>
 343 |             </xs:extension>
 344 |         </xs:complexContent>
 345 |     </xs:complexType>
 346 |     <xs:simpleType name="PlacementRankCV">
 347 |         <xs:annotation>
 348 |             <xs:documentation>
 349 |                 Controlled vocabulary for ranking placements
 350 |             </xs:documentation>
 351 |         </xs:annotation>
 352 |         <xs:restriction base="xs:string">
 353 |             <xs:enumeration value="BestAvailable">
 354 |                 <xs:annotation>
 355 |                     <xs:documentation>
 356 |                         This is the best placement available in the assembly.
 357 |                         (Regardless of whether it is submitted or remapped, single or multiple, first or second pass, genomic, cytogenetic, or HGVS)
 358 |                     </xs:documentation>
 359 |                 </xs:annotation>
 360 |             </xs:enumeration>
 361 |             <xs:enumeration value="NotBest">
 362 |                 <xs:annotation>
 363 |                     <xs:documentation>
 364 |                         There are better placements on the same assembly.    
 365 |                         Indicates that this is a remapped placement that does not have the best coverage score.
 366 |                     </xs:documentation>
 367 |                 </xs:annotation>
 368 |             </xs:enumeration>
 369 |             <xs:enumeration value="Ad-hocRemapping">
 370 |                 <xs:annotation>
 371 |                     <xs:documentation>
 372 |                         This remmapped placement was generated using an unknown remapper algorithm, therefore of low confidence.
 373 |                     </xs:documentation>
 374 |                 </xs:annotation>
 375 |             </xs:enumeration>
 376 |             <xs:enumeration value="Artifact">
 377 |                 <xs:annotation>
 378 |                     <xs:documentation>
 379 |                         This placement is a submitted artifact, therefore of low confidence.
 380 |                     </xs:documentation>
 381 |                 </xs:annotation>
 382 |             </xs:enumeration>
 383 |             <xs:enumeration value="NoPlacement">
 384 |                 <xs:annotation>
 385 |                     <xs:documentation>
 386 |                         There is no placement submitted or remapped on the assembly.
 387 |                     </xs:documentation>
 388 |                 </xs:annotation>
 389 |             </xs:enumeration>
 390 |         </xs:restriction>
 391 |     </xs:simpleType>
 392 |     <xs:simpleType name="PlacementsPerAssemblyCV">
 393 |         <xs:annotation>
 394 |             <xs:documentation>
 395 |                 Controlled vocabulary indicating if a placement is single or multiple within the same assembly.
 396 |             </xs:documentation>
 397 |         </xs:annotation>
 398 |         <xs:restriction base="xs:string">
 399 |             <xs:enumeration value="Single">
 400 |                 <xs:annotation>
 401 |                     <xs:documentation>
 402 |                         This is the only placement in this assembly.
 403 |                     </xs:documentation>
 404 |                 </xs:annotation>
 405 |             </xs:enumeration>
 406 |             <xs:enumeration value="Multiple">
 407 |                 <xs:annotation>
 408 |                     <xs:documentation>
 409 |                         This is one of multiple placements in the same assembly.
 410 |                     </xs:documentation>
 411 |                 </xs:annotation>
 412 |             </xs:enumeration>
 413 |         </xs:restriction>
 414 |     </xs:simpleType>
 415 |     <xs:simpleType name="RemapFailureCodeCV">
 416 |         <xs:annotation>
 417 |             <xs:documentation>
 418 |                 Controlled vocabulary for remap failures
 419 |             </xs:documentation>
 420 |         </xs:annotation>
 421 |         <xs:restriction base="xs:string">
 422 |             <xs:enumeration value="Expanded"/>
 423 |             <xs:enumeration value="LowCov"/>
 424 |             <xs:enumeration value="NoAlign"/>
 425 |             <xs:enumeration value="IDNotInAssembly"/>
 426 |             <xs:enumeration value="Other"/>
 427 |         </xs:restriction>
 428 |     </xs:simpleType>
 429 |     <xs:simpleType name="RecipientStatusCV">
 430 |         <xs:annotation>
 431 |             <xs:documentation>
 432 |                 Controlled vocabulary for placement Recipient                
 433 |             </xs:documentation>
 434 |         </xs:annotation>
 435 |         <xs:restriction base="xs:string">
 436 |             <xs:enumeration value="Ambiguous"/>
 437 |             <xs:enumeration value="Known"/>
 438 |         </xs:restriction>
 439 |     </xs:simpleType>
 440 |     <xs:simpleType name="ReferenceTypeCV">
 441 |         <xs:annotation>
 442 |             <xs:documentation>
 443 |                 Controlled vocabulary for reference_type               
 444 |             </xs:documentation>
 445 |         </xs:annotation>
 446 |         <xs:restriction base="xs:string">
 447 |             <xs:enumeration value="Assembly"/>
 448 |             <xs:enumeration value="Control tissue"/>
 449 |             <xs:enumeration value="Other"/>
 450 |             <xs:enumeration value="Sampleset"/>
 451 |             <xs:enumeration value="Sample"/>
 452 |         </xs:restriction>
 453 |     </xs:simpleType>
 454 |     <xs:simpleType name="SamplesetTypeCV">
 455 |         <xs:restriction base="xs:string">
 456 |             <xs:enumeration value="Case">
 457 |                 <xs:annotation>
 458 |                     <xs:documentation>
 459 |                         Sampleset was Case-set            
 460 |                     </xs:documentation>
 461 |                 </xs:annotation>
 462 |             </xs:enumeration>
 463 |             <xs:enumeration value="Control">
 464 |                 <xs:annotation>
 465 |                     <xs:documentation>
 466 |                         Sampleset was control-set               
 467 |                     </xs:documentation>
 468 |                 </xs:annotation>
 469 |             </xs:enumeration>
 470 |         </xs:restriction>
 471 |     </xs:simpleType>
 472 |     <xs:simpleType name="SeqTypeCV">
 473 |         <xs:annotation>
 474 |             <xs:documentation>Controlled vocabulary for sequence type    
 475 |             </xs:documentation>
 476 |         </xs:annotation>
 477 |         <xs:restriction base="xs:string">
 478 |             <xs:enumeration value="3_inner_flank">
 479 |                 <xs:annotation>
 480 |                     <xs:documentation>
 481 |                         last landmark affected by variant                 
 482 |                     </xs:documentation>
 483 |                 </xs:annotation>
 484 |             </xs:enumeration>
 485 |             <xs:enumeration value="3_outer_flank">
 486 |                 <xs:annotation>
 487 |                     <xs:documentation>
 488 |                         first unaffected landmark after variant                 
 489 |                     </xs:documentation>
 490 |                 </xs:annotation>
 491 |             </xs:enumeration>
 492 |             <xs:enumeration value="5_outer_flank">
 493 |                 <xs:annotation>
 494 |                     <xs:documentation>
 495 |                         last unaffected landmark before variant                 
 496 |                     </xs:documentation>
 497 |                 </xs:annotation>
 498 |             </xs:enumeration>
 499 |             <xs:enumeration value="5_inner_flank">
 500 |                 <xs:annotation>
 501 |                     <xs:documentation>
 502 |                         first landmark affected by variant                 
 503 |                     </xs:documentation>
 504 |                 </xs:annotation>
 505 |             </xs:enumeration>
 506 |             <xs:enumeration value="evidence_seq">
 507 |                 <xs:annotation>
 508 |                     <xs:documentation>
 509 |                         typically a sequence trace that shows the variant breakpoint, and which was used to make the variant call                 
 510 |                     </xs:documentation>
 511 |                 </xs:annotation>
 512 |             </xs:enumeration>
 513 |             <xs:enumeration value="support_seq">
 514 |                 <xs:annotation>
 515 |                     <xs:documentation>
 516 |                         typically the ID(s) of a probe(s) which were observed to have increased or decreased signal intensity, and so were used to call the variant                 
 517 |                     </xs:documentation>
 518 |                 </xs:annotation>
 519 |             </xs:enumeration>
 520 |             <xs:enumeration value="variant_seq">
 521 |                 <xs:annotation>
 522 |                     <xs:documentation>
 523 |                         the actual variant sequence; can either be literal sequence under 100bp, or a GENBANK accession containing the literal sequence if greater than 100bp                 
 524 |                     </xs:documentation>
 525 |                 </xs:annotation>
 526 |             </xs:enumeration>
 527 |         </xs:restriction>
 528 |     </xs:simpleType>
 529 |     <xs:simpleType name="SexCV">
 530 |         <xs:annotation>
 531 |             <xs:documentation>
 532 |                 Controlled vocabulary for subject Sex                  
 533 |             </xs:documentation>
 534 |         </xs:annotation>
 535 |         <xs:restriction base="xs:string">
 536 |             <xs:enumeration value="Female"/>
 537 |             <xs:enumeration value="Male"/>
 538 |             <xs:enumeration value="Unknown"/>
 539 |         </xs:restriction>
 540 |     </xs:simpleType>
 541 |     <xs:simpleType name="StrandTypeCV">
 542 |         <xs:annotation>
 543 |             <xs:documentation>
 544 |                 Controlled vocabulary for strand Type                 
 545 |             </xs:documentation>
 546 |         </xs:annotation>
 547 |         <xs:restriction base="xs:string">
 548 |             <xs:enumeration value="+">
 549 |                 <xs:annotation>
 550 |                     <xs:documentation>
 551 |                         + strand             
 552 |                     </xs:documentation>
 553 |                 </xs:annotation>
 554 |             </xs:enumeration>
 555 |             <xs:enumeration value="-">
 556 |                 <xs:annotation>
 557 |                     <xs:documentation>
 558 |                         - strand              
 559 |                     </xs:documentation>
 560 |                 </xs:annotation>
 561 |             </xs:enumeration>
 562 |             <xs:enumeration value="not reported">
 563 |                 <xs:annotation>
 564 |                     <xs:documentation>
 565 |                         This value can be assigned by the converter if a value for strand is expected but was not submitted.
 566 |                     </xs:documentation>
 567 |                 </xs:annotation>
 568 |             </xs:enumeration>
 569 |         </xs:restriction>
 570 |     </xs:simpleType>
 571 |     <xs:simpleType name="StudyTypeCV">
 572 |         <xs:annotation>
 573 |             <xs:documentation>
 574 |                 Controlled vocabulary for Study Type                 
 575 |             </xs:documentation>
 576 |         </xs:annotation>
 577 |         <xs:restriction base="xs:string">
 578 |             <xs:enumeration value="Case-Control">
 579 |                 <xs:annotation>
 580 |                     <xs:documentation>
 581 |                         Comparison between healthy and diseased individuals.               
 582 |                     </xs:documentation>
 583 |                 </xs:annotation>
 584 |             </xs:enumeration>
 585 |             <xs:enumeration value="Case-Set">
 586 |                 <xs:annotation>
 587 |                     <xs:documentation>
 588 |                         Disease-associated variation.                
 589 |                     </xs:documentation>
 590 |                 </xs:annotation>
 591 |             </xs:enumeration>
 592 |             <xs:enumeration value="Collection">
 593 |                 <xs:annotation>
 594 |                     <xs:documentation>
 595 |                         A collection of variation                
 596 |                     </xs:documentation>
 597 |                 </xs:annotation>
 598 |             </xs:enumeration>
 599 |             <xs:enumeration value="Control Set">
 600 |                 <xs:annotation>
 601 |                     <xs:documentation>
 602 |                         Variation in healthy population.                 
 603 |                     </xs:documentation>
 604 |                 </xs:annotation>
 605 |             </xs:enumeration>
 606 |             <xs:enumeration value="Somatic">
 607 |                 <xs:annotation>
 608 |                     <xs:documentation>
 609 |                         Somatic Variation               
 610 |                     </xs:documentation>
 611 |                 </xs:annotation>
 612 |             </xs:enumeration>
 613 |             <xs:enumeration value="Tumor vs. Matched-Normal">
 614 |                 <xs:annotation>
 615 |                     <xs:documentation>
 616 |                         Somatic variation detected from comparison of tumor to healthy tissue from the same individual.                 
 617 |                     </xs:documentation>
 618 |                 </xs:annotation>
 619 |             </xs:enumeration>
 620 |         </xs:restriction>
 621 |     </xs:simpleType>
 622 |     <xs:simpleType name="SubjectAgeUnitsCV">
 623 |         <xs:annotation>
 624 |             <xs:documentation>
 625 |                 Controlled vocabulary for Study Type                 
 626 |             </xs:documentation>
 627 |         </xs:annotation>
 628 |         <xs:restriction base="xs:string">
 629 |             <xs:enumeration value="Day">
 630 |                 <xs:annotation>
 631 |                     <xs:documentation>
 632 |                         Subject Age in Days              
 633 |                     </xs:documentation>
 634 |                 </xs:annotation>
 635 |             </xs:enumeration>
 636 |             <xs:enumeration value="Week">
 637 |                 <xs:annotation>
 638 |                     <xs:documentation>
 639 |                         Subject Age in Weeks                
 640 |                     </xs:documentation>
 641 |                 </xs:annotation>
 642 |             </xs:enumeration>
 643 |             <xs:enumeration value="Month">
 644 |                 <xs:annotation>
 645 |                     <xs:documentation>
 646 |                         Subject Age in Months                 
 647 |                     </xs:documentation>
 648 |                 </xs:annotation>
 649 |             </xs:enumeration>
 650 |             <xs:enumeration value="Year">
 651 |                 <xs:annotation>
 652 |                     <xs:documentation>
 653 |                         Subject Age in Years           
 654 |                     </xs:documentation>
 655 |                 </xs:annotation>
 656 |             </xs:enumeration>
 657 |             <xs:enumeration value="GDay">
 658 |                 <xs:annotation>
 659 |                     <xs:documentation>
 660 |                         Subject Gestational Age in Days                
 661 |                     </xs:documentation>
 662 |                 </xs:annotation>
 663 |             </xs:enumeration>
 664 |             <xs:enumeration value="GWeek">
 665 |                 <xs:annotation>
 666 |                     <xs:documentation>
 667 |                         Subject Gestational Age in Weeks                 
 668 |                     </xs:documentation>
 669 |                 </xs:annotation>
 670 |             </xs:enumeration>
 671 |             <xs:enumeration value="GMonth">
 672 |                 <xs:annotation>
 673 |                     <xs:documentation>
 674 |                         Subject Gestational Age in Months                
 675 |                     </xs:documentation>
 676 |                 </xs:annotation>
 677 |             </xs:enumeration>
 678 |         </xs:restriction>
 679 |     </xs:simpleType>
 680 |     <xs:simpleType name="ValidationResultCV">
 681 |         <xs:annotation>
 682 |             <xs:documentation>
 683 |                 Controlled vocabulary for Validation result                  
 684 |             </xs:documentation>
 685 |         </xs:annotation>
 686 |         <xs:restriction base="xs:string">
 687 |             <xs:enumeration value="Fail"/>
 688 |             <xs:enumeration value="Pass"/>
 689 |             <xs:enumeration value="Inconclusive"/>
 690 |         </xs:restriction>
 691 |     </xs:simpleType>
 692 |     <xs:simpleType name="VariantCallTypeCV">
 693 |         <xs:annotation>
 694 |             <xs:documentation>
 695 |                 Controlled vocabulary for Variant Call
 696 |                 Type                  
 697 |             </xs:documentation>
 698 |         </xs:annotation>
 699 |         <xs:restriction base="xs:string">
 700 |             <xs:enumeration value="complex substitution"/>
 701 |             <xs:enumeration value="copy-neutral loss of heterozygosity"/>
 702 |             <xs:enumeration value="copy number gain"/>
 703 |             <xs:enumeration value="copy number loss"/>
 704 |             <xs:enumeration value="copy number variation"/>
 705 |             <xs:enumeration value="deletion"/>
 706 |             <xs:enumeration value="mobile element deletion"/>
 707 |             <xs:enumeration value="alu deletion"/>
 708 |             <xs:enumeration value="line1 deletion"/>
 709 |             <xs:enumeration value="sva deletion"/>
 710 |             <xs:enumeration value="herv deletion"/>
 711 |             <xs:enumeration value="duplication"/>
 712 |             <xs:enumeration value="delins"/>
 713 |             <xs:enumeration value="insertion"/>
 714 |             <xs:enumeration value="interchromosomal translocation"/>
 715 |             <xs:enumeration value="intrachromosomal translocation"/>
 716 |             <xs:enumeration value="inversion"/>
 717 |             <xs:enumeration value="mobile element insertion"/>
 718 |             <xs:enumeration value="alu insertion"/>
 719 |             <xs:enumeration value="herv insertion"/>
 720 |             <xs:enumeration value="line1 insertion"/>
 721 |             <xs:enumeration value="sva insertion"/>
 722 |             <xs:enumeration value="novel sequence insertion"/>
 723 |             <xs:enumeration value="sequence alteration"/>
 724 |             <xs:enumeration value="short tandem repeat"/>
 725 |             <xs:enumeration value="tandem duplication"/>
 726 |         </xs:restriction>
 727 |     </xs:simpleType>
 728 |     <xs:simpleType name="VariantCallZygosityCV">
 729 |         <xs:annotation>
 730 |             <xs:documentation>
 731 |                 Controlled vocabulary for Variant_call Zygosity                  
 732 |             </xs:documentation>
 733 |         </xs:annotation>
 734 |         <xs:restriction base="xs:string">
 735 |             <xs:enumeration value="Hemizygous">
 736 |                 <xs:annotation>
 737 |                     <xs:documentation>
 738 |                         Hemizygous variant_call                
 739 |                     </xs:documentation>
 740 |                 </xs:annotation>
 741 |             </xs:enumeration>
 742 |             <xs:enumeration value="Heterozygous">
 743 |                 <xs:annotation>
 744 |                     <xs:documentation>
 745 |                         Heterozygous variant_call               
 746 |                     </xs:documentation>
 747 |                 </xs:annotation>
 748 |             </xs:enumeration>
 749 |             <xs:enumeration value="Homozygous">
 750 |                 <xs:annotation>
 751 |                     <xs:documentation>
 752 |                         Homozygous variant_call                
 753 |                     </xs:documentation>
 754 |                 </xs:annotation>
 755 |             </xs:enumeration>
 756 |         </xs:restriction>
 757 |     </xs:simpleType>
 758 |     <xs:simpleType name="VariantRegionTypeCV">
 759 |         <xs:annotation>
 760 |             <xs:documentation>
 761 |                 Controlled vocabulary for Variant Region 
 762 |                 Type                  
 763 |             </xs:documentation>
 764 |         </xs:annotation>
 765 |         <xs:restriction base="xs:string">
 766 |             <xs:enumeration value="complex substitution"/>
 767 |             <xs:enumeration value="complex chromosomal rearrangement"/>
 768 |             <xs:enumeration value="copy-neutral loss of heterozygosity"/>
 769 |             <xs:enumeration value="copy number variation"/>
 770 |             <xs:enumeration value="delins"/>
 771 |             <xs:enumeration value="insertion"/>
 772 |             <xs:enumeration value="inversion"/>
 773 |             <xs:enumeration value="mobile element insertion"/>
 774 |             <xs:enumeration value="mobile element deletion"/>
 775 |             <xs:enumeration value="novel sequence insertion"/>
 776 |             <xs:enumeration value="sequence alteration"/>
 777 |             <xs:enumeration value="short tandem repeat"/>
 778 |             <xs:enumeration value="tandem duplication"/>
 779 |             <xs:enumeration value="translocation"/>
 780 |         </xs:restriction>
 781 |     </xs:simpleType>
 782 | 
 783 |     <xs:complexType name="LinkType">
 784 |         <xs:attribute name="db" type="LinkDbCV" use="required">
 785 |             <xs:annotation>
 786 |                 <xs:documentation>
 787 |                     Database name from controlled vocabulary 
 788 |                 </xs:documentation>
 789 |             </xs:annotation>
 790 |         </xs:attribute>
 791 |         <xs:attribute name="id" type="xs:string" use="required">
 792 |             <xs:annotation>
 793 |                 <xs:documentation>
 794 |                     Database ID
 795 |                 </xs:documentation>
 796 |             </xs:annotation>
 797 |         </xs:attribute>
 798 |         <xs:attribute name="invalid" type="xs:boolean" use="optional">
 799 |             <xs:annotation>
 800 |                 <xs:documentation>
 801 |                     Indicates the link is not valid.                    
 802 |                 </xs:documentation>
 803 |             </xs:annotation>
 804 |         </xs:attribute>
 805 |     </xs:complexType>
 806 |     
 807 |     <xs:complexType name="URLType">
 808 |         <xs:attribute name="url" type="xs:anyURI" use="required">
 809 |         </xs:attribute>
 810 |         <xs:attribute name="invalid" type="xs:boolean" use="optional">
 811 |             <xs:annotation>
 812 |                 <xs:documentation>
 813 |                     Indicates the URL is not valid.                    
 814 |                 </xs:documentation>
 815 |             </xs:annotation>
 816 |         </xs:attribute>
 817 |     </xs:complexType>
 818 |     
 819 |     <xs:complexType name="PlacementType">
 820 |         <xs:sequence>
 821 |             <xs:element name="GENOME" minOccurs="0" maxOccurs="1">
 822 |                 <xs:annotation>
 823 |                     <xs:documentation>Placement of the variant to a sequenced genome</xs:documentation>
 824 |                 </xs:annotation>
 825 |                 <xs:complexType>
 826 |                     <xs:attribute name="assembly" type="xs:string" use="required"/>
 827 |                     <xs:attribute name="chr_name" type="xs:string" use="optional">
 828 |                         <xs:annotation>
 829 |                             <xs:documentation>chromosome name</xs:documentation>
 830 |                         </xs:annotation>
 831 |                     </xs:attribute>
 832 |                     <xs:attribute name="contig_accession" type="xs:string" use="optional">
 833 |                         <xs:annotation>
 834 |                             <xs:documentation>contig accession</xs:documentation>
 835 |                         </xs:annotation>
 836 |                     </xs:attribute>
 837 |                     <xs:attribute name="chr_accession" type="xs:string" use="optional">
 838 |                         <xs:annotation>
 839 |                             <xs:documentation>chromosome accession</xs:documentation>
 840 |                         </xs:annotation>
 841 |                     </xs:attribute>
 842 |                     <xs:attribute name="outer_start" type="xs:positiveInteger" use="optional"/>
 843 |                     <xs:attribute name="start" type="xs:positiveInteger" use="optional"/>
 844 |                     <xs:attribute name="inner_start" type="xs:positiveInteger" use="optional"/>
 845 |                     <xs:attribute name="stop" type="xs:positiveInteger" use="optional"/>
 846 |                     <xs:attribute name="inner_stop" type="xs:positiveInteger" use="optional"/>
 847 |                     <xs:attribute name="outer_stop" type="xs:positiveInteger"/>
 848 |                     <xs:attribute name="ciposleft" type="xs:nonNegativeInteger" use="optional">
 849 |                         <xs:annotation>
 850 |                             <xs:documentation>The left confidence interval around start.  Use instead of outer_start when there are confidence intervals.</xs:documentation>
 851 |                         </xs:annotation>
 852 |                     </xs:attribute>
 853 |                     <xs:attribute name="ciposright" type="xs:nonNegativeInteger" use="optional">
 854 |                         <xs:annotation>
 855 |                             <xs:documentation>The right confidence interval around start.  Use instead of inner_start when there are confidence intervals.</xs:documentation>
 856 |                         </xs:annotation>
 857 |                     </xs:attribute>
 858 |                     <xs:attribute name="ciendleft" type="xs:nonNegativeInteger" use="optional">
 859 |                         <xs:annotation>
 860 |                             <xs:documentation>The left confidence interval around stop.  Use instead of inner_stop when there are confidence intervals.</xs:documentation>
 861 |                         </xs:annotation>
 862 |                     </xs:attribute>
 863 |                     <xs:attribute name="ciendright" type="xs:nonNegativeInteger" use="optional">
 864 |                         <xs:annotation>
 865 |                             <xs:documentation>The right confidence interval around stop.  Use instead of outer_stop when there are confidence intervals.</xs:documentation>
 866 |                         </xs:annotation>
 867 |                     </xs:attribute>
 868 |                     <xs:attribute name="remap_score" type="xs:float" use="optional"/>
 869 |                     <xs:attribute name="strand" type="StrandTypeCV" use="optional"/>
 870 |                     <xs:attribute name="assembly_unit" type="xs:string" use="optional">
 871 |                         <xs:annotation>
 872 |                             <xs:documentation>The assembly unit to which the mapped_id belongs</xs:documentation>
 873 |                         </xs:annotation>
 874 |                     </xs:attribute>
 875 |                     <xs:attribute name="alignment" type="AlignmentCV" use="optional">
 876 |                         <xs:annotation>
 877 |                             <xs:documentation>First Pass means the remapping is based on the 'First Pass' or reciprocal best hit alignments. 'Second Pass' means the remapping is based on the non-reciprocal best hit alignments</xs:documentation>
 878 |                         </xs:annotation>
 879 |                     </xs:attribute>
 880 |                     <xs:attribute name="remap_failure_code" type="RemapFailureCodeCV" use="optional"/>
 881 |                     <xs:attribute name="placement_rank" type="PlacementRankCV" use="optional"/>
 882 |                     <xs:attribute name="placements_per_assembly" type="PlacementsPerAssemblyCV"
 883 |                         use="optional"/>
 884 |                     <xs:attribute name="remap_diff_chr" use="optional" type="xs:boolean">
 885 |                         <xs:annotation>
 886 |                             <xs:documentation>1=remapped placement is on a different AC_ or NC_ chromosome than the source chromosome</xs:documentation>
 887 |                         </xs:annotation>
 888 |                     </xs:attribute>
 889 |                     <xs:attribute name="remap_best_within_cluster" use="optional" type="xs:boolean">
 890 |                         <xs:annotation>
 891 |                             <xs:documentation>1=remapped placement was best-scoring placement within a cluster/overlap/subset on same chromosome and alignment (First Pass or Second Pass), and other remapped placements were dropped</xs:documentation>
 892 |                         </xs:annotation>
 893 |                     </xs:attribute>
 894 |                 </xs:complexType>
 895 |             </xs:element>
 896 |             <xs:element name="CYTOGENETIC" minOccurs="0" maxOccurs="1">
 897 |                 <xs:annotation>
 898 |                     <xs:documentation>Placement of the variant to a cytogenetic band location</xs:documentation>
 899 |                 </xs:annotation>
 900 |                 <xs:complexType>
 901 |                     <xs:attribute name="taxonomy_id" use="required" type="xs:string">
 902 |                         <xs:annotation>
 903 |                             <xs:documentation>NCBI Taxonomy ID (https://www.ncbi.nlm.nih.gov/taxonomy)</xs:documentation>
 904 |                         </xs:annotation>
 905 |                     </xs:attribute>
 906 |                     <xs:attribute name="cytoband" use="required" type="xs:string">
 907 |                         <xs:annotation>
 908 |                             <xs:documentation>eg 7p12-7p11.2</xs:documentation>
 909 |                         </xs:annotation>
 910 |                     </xs:attribute>
 911 |                 </xs:complexType>
 912 |             </xs:element>
 913 |         </xs:sequence>
 914 |         <xs:attribute name="alt_status" type="RecipientStatusCV">
 915 |             <xs:annotation>
 916 |                 <xs:documentation>indicate status for alternate placement</xs:documentation>
 917 |             </xs:annotation>
 918 |         </xs:attribute>
 919 |         <xs:attribute name="placement_method" type="GenomicPlacementMethodCV" use="optional"/>
 920 |         <xs:attribute name="breakpoint_order" use="optional" type="BreakpointPairCV"/>
 921 |     </xs:complexType>
 922 |     <xs:complexType name="CallPlacementType">
 923 |         <xs:annotation>
 924 |             <xs:documentation>Variant Calls have an HGVS expression associated with a placement</xs:documentation>
 925 |         </xs:annotation>
 926 |         <xs:complexContent>
 927 |             <xs:extension base="PlacementType">
 928 |                 <xs:attribute name="hgvs_name" type="xs:string" use="optional"/>
 929 |             </xs:extension>
 930 |         </xs:complexContent>
 931 |     </xs:complexType>
 932 |     <xs:complexType name="RegionPlacementType">
 933 |         <xs:annotation>
 934 |             <xs:documentation>Variant Regions may have variant_call_id, mutation_order, and mutation_molecule associated with a placement</xs:documentation>
 935 |         </xs:annotation>
 936 |         <xs:complexContent>
 937 |             <xs:extension base="PlacementType">
 938 |                 <xs:attribute name="variant_call_id" type="xs:string" use="optional"/>
 939 |                 <xs:attribute name="mutation_order" type="xs:positiveInteger" use="optional"/>
 940 |                 <xs:attribute name="mutation_molecule" type="xs:string" use="optional"/>
 941 |             </xs:extension>
 942 |         </xs:complexContent>
 943 |     </xs:complexType>
 944 |     <xs:complexType name="ContactType">
 945 |         <xs:attribute name="contact_role" type="ContactRoleCV" use="required"> </xs:attribute>
 946 |         <xs:attribute name="first_name" use="optional" type="xs:string">
 947 |             <xs:annotation>
 948 |                 <xs:documentation>
 949 |                     The contact's first name. Must have either a first_name or a last_name.
 950 |                 </xs:documentation>
 951 |             </xs:annotation>
 952 |         </xs:attribute>
 953 |         <xs:attribute name="last_name" use="optional" type="xs:string"> </xs:attribute>
 954 |         <xs:attribute name="contact_email" use="optional" type="xs:string">
 955 |             <xs:annotation>
 956 |                 <xs:documentation>The email is optional in the submission because it can be obtained from myncbi_id.
 957 |                 </xs:documentation>
 958 |             </xs:annotation>
 959 |         </xs:attribute>
 960 |         <xs:attribute name="myncbi_id" type="xs:string">
 961 |             <xs:annotation>
 962 |                 <xs:documentation>MyNCBI login system ID
 963 | (https://www.ncbi.nlm.nih.gov/myncbi)</xs:documentation>
 964 |             </xs:annotation>
 965 |         </xs:attribute>
 966 |         <xs:attribute name="contact_phone" type="xs:string"/>
 967 |         <xs:attribute name="affiliation_name" use="required" type="xs:string"> </xs:attribute>
 968 |         <xs:attribute name="affiliation_address" type="xs:string"/>
 969 | 	<xs:attribute name="affiliation_url" type="xs:anyURI"/>
 970 | 	<xs:attribute name="affiliation_url_invalid" type="xs:boolean"/>
 971 |     </xs:complexType>
 972 |     <xs:complexType name="LibraryType">
 973 |         <xs:complexContent>
 974 |             <xs:extension base="LinkType">
 975 |                 <xs:attribute name="abbrev" type="xs:string" use="required"/>
 976 |             </xs:extension>
 977 |         </xs:complexContent>
 978 |     </xs:complexType>
 979 |     <xs:complexType name="PhenotypeType">
 980 |         <xs:sequence>
 981 |             <xs:element name="DESCRIPTION" minOccurs="0" maxOccurs="1" type="xs:string">
 982 |                 <xs:annotation>
 983 |                     <xs:documentation>optional phenotype description, although standard terms are preferred                  
 984 |                     </xs:documentation>
 985 |                 </xs:annotation>
 986 |             </xs:element>
 987 |             <xs:element maxOccurs="unbounded" minOccurs="0" name="LINK" type="PhenotypeLink"/>
 988 |         </xs:sequence>
 989 |     </xs:complexType>
 990 |     <xs:complexType name="SeqType">
 991 |         <xs:complexContent>
 992 |             <xs:extension base="LinkType">
 993 |                 <xs:attribute name="sequence_type" type="SeqTypeCV" use="required"/>
 994 |             </xs:extension>
 995 |         </xs:complexContent>
 996 |     </xs:complexType>
 997 | 
 998 |     <xs:element name="SUBMISSION">
 999 |         <xs:annotation>
1000 |             <xs:documentation>Top Level Submission Package</xs:documentation>
1001 |         </xs:annotation>
1002 |         <xs:complexType>
1003 |             <xs:sequence>
1004 |                 <xs:element ref="CONTACT" minOccurs="0" maxOccurs="unbounded"/>
1005 |                 <xs:element ref="STUDY" minOccurs="0" maxOccurs="1"/>
1006 |                 <xs:element ref="SUBJECT" minOccurs="0" maxOccurs="unbounded"/>
1007 |                 <xs:element ref="SAMPLESET" minOccurs="0" maxOccurs="unbounded"/>
1008 |                 <xs:element ref="SAMPLE" minOccurs="0" maxOccurs="unbounded"/>
1009 |                 <xs:element ref="EXPERIMENT" minOccurs="0" maxOccurs="unbounded"/>
1010 |                 <xs:element ref="VARIANT_CALL" minOccurs="0" maxOccurs="unbounded"/>
1011 |                 <xs:element ref="VARIANT_REGION" minOccurs="0" maxOccurs="unbounded"/>
1012 |                 <xs:element ref="GENOTYPE" minOccurs="0" maxOccurs="unbounded"/>
1013 |                 <xs:element ref="DELETED_VARIANTS" minOccurs="0" maxOccurs="unbounded"/>
1014 |             </xs:sequence>
1015 |             <xs:attribute name="dbvar_schema_version" use="optional">
1016 |                 <xs:annotation>
1017 |                     <xs:documentation>version of the XSD</xs:documentation>
1018 |                 </xs:annotation>
1019 |                 <xs:simpleType>
1020 |                     <xs:annotation>
1021 |                         <xs:documentation>
1022 |                             Versions used in submission files.
1023 |                             Format: Major.Component.Update                 
1024 |                             Major     = structural change in the model.
1025 |                             Component = change such as addition of a new object
1026 |                             Update    = minor change such as addition of CF type or update/addition/removal of a field.  
1027 |                         </xs:documentation>
1028 |                     </xs:annotation>
1029 |                     <xs:restriction base="xs:string">
1030 |                         <xs:enumeration value="2.0.0">
1031 |                             <xs:annotation>
1032 |                                 <xs:documentation>
1033 |                                     May 18, 2010
1034 |                                     Added SUBMISSION/version.
1035 |                                     Added STRUCTVAR/VARIANT_SET/VARIANT/MERGED_VARIANT/id for merged variants.
1036 |                                     Changed ANALYSIS/id, METHOD/id to positiveInteger in order to agree with exchange.
1037 |                                 </xs:documentation>
1038 |                             </xs:annotation>
1039 |                         </xs:enumeration>
1040 |                         <xs:enumeration value="2.1.0">
1041 |                             <xs:annotation>
1042 |                                 <xs:documentation>
1043 |                                     Jun 8, 2010
1044 |                                     Added HPO to PhenotypeType.
1045 |                                     Replaced STRUCTVAR/VARIANT_SET/VARIANT/ALLELE/phenotype with STRUCTVAR/VARIANT_SET/VARIANT/ALLELE/PHENOTYPE.
1046 |                                     Changed STRUCTVAR/VARIANT_SET/VARIANT/ALLELE string to STRUCTVAR/VARIANT_SET/VARIANT/ALLELE/DESCRIPTION.
1047 |                                 </xs:documentation>
1048 |                             </xs:annotation>
1049 |                         </xs:enumeration>
1050 |                         <xs:enumeration value="2.1.1">
1051 |                             <xs:annotation>
1052 |                                 <xs:documentation>
1053 |                                     Jun 24, 2010
1054 |                                     Added STUDY/NCBI_submission_id
1055 |                                 </xs:documentation>
1056 |                             </xs:annotation>
1057 |                         </xs:enumeration>
1058 |                         <xs:enumeration value="2.1.2">
1059 |                             <xs:annotation>
1060 |                                 <xs:documentation>
1061 |                                     July 26, 2010
1062 |                                     Add Curated to StudyType.
1063 |                                     Add LSDB, MassSpec, Optical mapping to MethodTypeCV.
1064 |                                     Added VARIANT/PLACEMENT/GENOME/placement_method, GenomicPlacementMethodCV. 
1065 |                                     Moved STRUCTVAR/VARIANT_SET/VARIANT/ALLELE/DESCRIPTION to STRUCTVAR/VARIANT_SET/VARIANT/DESCRIPTION.
1066 |                                     Removed STRUCTVAR/VARIANT_SET/VARIANT/notes, since DESCRIPTION will be used instead.
1067 |                                     Added Library to SampleTypeCV, since it is in Exchange.xsd.
1068 |                                     Added definitions to StudyTypeCV.
1069 |                                 </xs:documentation>
1070 |                             </xs:annotation>
1071 |                         </xs:enumeration>
1072 |                         <xs:enumeration value="2.1.3">
1073 |                             <xs:annotation>
1074 |                                 <xs:documentation>
1075 |                                     August 12, 2010
1076 |                                     Changed start, outer_start to nonNegativeInteger to allow for base 0.
1077 |                                     Changed start, stop to optional for studies that only have outer_start, outer_stop.
1078 |                                 </xs:documentation>
1079 |                             </xs:annotation>
1080 |                         </xs:enumeration>
1081 |                         <xs:enumeration value="2.1.4">
1082 |                             <xs:annotation>
1083 |                                 <xs:documentation>
1084 |                                     October 28, 2010
1085 |                                     Added inner_start, inner_stop to placements.
1086 |                                     Added Genomic to GenomicPlacementMethodCV.
1087 |                                     Added SUBJECT/PEDIGREE/chromosome_complement.
1088 |                                     Added Karyotype to MethodCV for validation.
1089 |                                     Added AssemblyCV and use it in ANALYSIS/REFERENCE/assembly and PLACEMENT/GENOME/assembly.
1090 |                                     Removed STRUCTVAR/base.
1091 |                                 </xs:documentation>
1092 |                             </xs:annotation>
1093 |                         </xs:enumeration>
1094 |                         <xs:enumeration value="2.1.5">
1095 |                             <xs:annotation>
1096 |                                 <xs:documentation>
1097 |                                     November 18, 2010
1098 |                                     Per STV-604, removed these from AlleleTypeCV:
1099 |                                     Amplification, CNV, Deletion, DelIns, Duplication, Gain+Loss, LOH, Ring, Translocation.
1100 |                                     Per STV-619, added ClinicalSignificanceCV.
1101 |                                     Per STV-723, added ALLELE/loss_of_heterozygosity.
1102 |                                 </xs:documentation>
1103 |                             </xs:annotation>
1104 |                         </xs:enumeration>
1105 |                         <xs:enumeration value="2.1.6">
1106 |                             <xs:annotation>
1107 |                                 <xs:documentation>
1108 |                                     December 3, 2010
1109 |                                     Set VARIANT_SET to optional, since ISCA will submit instances to existing variants.  This also allows generation of temporary xml files with only instances.
1110 |                                     STV-731: Add dbSNP to MethodTypeCV.
1111 |                                     STV-732: Add "Conventional CGH" to MethodTypeCV.                                
1112 |                                 </xs:documentation>
1113 |                             </xs:annotation>
1114 |                         </xs:enumeration>
1115 |                         <xs:enumeration value="2.1.7">
1116 |                             <xs:annotation>
1117 |                                 <xs:documentation>
1118 |                                     December 20, 2010  
1119 |                                     STV-622: added GRCh37.p1, GRCh37.p2.                                
1120 |                                 </xs:documentation>
1121 |                             </xs:annotation>
1122 |                         </xs:enumeration>
1123 |                         <xs:enumeration value="2.1.8">
1124 |                             <xs:annotation>
1125 |                                 <xs:documentation>
1126 |                                     January 19, 2011  
1127 |                                     VLOAD-106: added Sscrofa9.  
1128 |                                     STV-761: added SAMPLE/SAMPLESET/id.   
1129 |                                     STV-709: Allow only 1 ANALYSIS/REFERENCE.                                  
1130 |                                 </xs:documentation>
1131 |                             </xs:annotation>
1132 |                         </xs:enumeration>
1133 |                         <xs:enumeration value="2.1.9">
1134 |                             <xs:annotation>
1135 |                                 <xs:documentation>
1136 |                                     February 17, 2011  
1137 |                                     STV-782: Removed ANALYSIS/REFERENCE/POOLED.
1138 |                                     Allow ANALYSIS/REFERENCE/SAMPLE and SAMPLESET to be repeated. 
1139 |                                     STV-783: Added VARIANT/ALLELE/mode_of_inheritence.                                    
1140 |                                 </xs:documentation>
1141 |                             </xs:annotation>
1142 |                         </xs:enumeration>
1143 |                         <xs:enumeration value="2.1.10">
1144 |                             <xs:annotation>
1145 |                                 <xs:documentation>
1146 |                                     March 14, 2011  
1147 |                                     VLOAD-100: added Btau_4.0.                                   
1148 |                                 </xs:documentation>
1149 |                             </xs:annotation>
1150 |                         </xs:enumeration>
1151 |                         <xs:enumeration value="2.1.11">
1152 |                             <xs:annotation>
1153 |                                 <xs:documentation>
1154 |                                     April 19, 2011  
1155 |                                     VLOAD-13: Although SUBMISSION/submission_id is required in the Exchange.xsd, STUDY/NCBI_submission_id should be optional since it is not included in FTP files.                                   
1156 |                                     VLOAD-128, STV-797: Added STUDY/ALIASES/alias.
1157 |                                     VLOAD-129: Made sampleset id's integer.
1158 |                                     VLOAD-132: Replaced Everted with "Tandem duplication" in AlleleTypeCV.
1159 |                                 </xs:documentation>
1160 |                             </xs:annotation>
1161 |                         </xs:enumeration>
1162 |                         <xs:enumeration value="2.1.12">
1163 |                             <xs:annotation>
1164 |                                 <xs:documentation>
1165 |                                     July 7, 2011  
1166 |                                     STV-674: Changed values in GenomePlacementMethodCV.
1167 |                                     STV-888: Added PlacementType/remap_score.
1168 |                                     STV-731, STV-800: Removed 'Sequence alingnment', 'Read-depth analysis', 'Paired-end mapping', 'SNP genotyping analysis',
1169 |                                             'Composite Approach', dbSNP, LSDB from MethodTypeCV.
1170 |                                 </xs:documentation>
1171 |                             </xs:annotation>
1172 |                         </xs:enumeration>
1173 |                         <xs:enumeration value="3.0.0">
1174 |                             <!-- LATEST VERSION: 3.0.0 -->
1175 |                             <xs:annotation>
1176 |                                 <xs:documentation>
1177 |                                     August 24, 2011  
1178 |                                     STV-950: Major updates for new submission template. 
1179 |                                 </xs:documentation>
1180 |                             </xs:annotation>
1181 |                         </xs:enumeration>
1182 |                     </xs:restriction>
1183 |                 </xs:simpleType>
1184 |             </xs:attribute>
1185 |             <xs:attribute name="vload_id" use="required" type="xs:string">
1186 |                 <xs:annotation>
1187 |                     <xs:documentation>
1188 |                         Jira issue number for the study, i.e. VLOAD-123.           
1189 |                     </xs:documentation>
1190 |                 </xs:annotation>
1191 |             </xs:attribute>
1192 |             <xs:attribute name="study_id" use="required" type="xs:string">
1193 |                 <xs:annotation>
1194 |                     <xs:documentation>
1195 |                         Submitter study_id in the form of 'AuthorYear'                       
1196 |                     </xs:documentation>
1197 |                 </xs:annotation>
1198 |             </xs:attribute>
1199 |         </xs:complexType>
1200 |     </xs:element>
1201 | 
1202 |     <xs:element name="CONTACT" type="ContactType">
1203 |         <xs:annotation>
1204 |             <xs:documentation>
1205 |                 Submitter or other contact.
1206 |             </xs:documentation>
1207 |         </xs:annotation>
1208 |     </xs:element>
1209 | 
1210 |     <xs:element name="STUDY">
1211 |         <xs:annotation>
1212 |             <xs:documentation>
1213 |                 Details of study         
1214 |             </xs:documentation>
1215 |         </xs:annotation>
1216 |         <xs:complexType>
1217 |             <xs:sequence>
1218 |                 <xs:element name="DESCRIPTION" type="xs:string" maxOccurs="1" minOccurs="1"/>
1219 |                 <xs:element name="ORGANISM" minOccurs="1" maxOccurs="unbounded">
1220 |                     <xs:complexType>
1221 |                         <xs:attribute name="taxonomy_id" use="required" type="xs:positiveInteger">
1222 |                             <xs:annotation>
1223 |                                 <xs:documentation>
1224 |                                     NCBI Taxonomy ID (https://www.ncbi.nlm.nih.gov/taxonomy)                                 
1225 |                                 </xs:documentation>
1226 |                             </xs:annotation>
1227 |                         </xs:attribute>
1228 |                     </xs:complexType>
1229 |                 </xs:element>
1230 |                 <xs:element name="PUBLICATION" minOccurs="0" maxOccurs="unbounded">
1231 |                     <xs:complexType>
1232 |                         <xs:attribute name="pubmed_id" use="required" type="xs:positiveInteger">
1233 |                             <xs:annotation>
1234 |                                 <xs:documentation>
1235 |                                     NCBI PubMed ID (https://www.ncbi.nlm.nih.gov/pubmed/)                                    
1236 |                                 </xs:documentation>
1237 |                             </xs:annotation>
1238 |                         </xs:attribute>
1239 |                     </xs:complexType>
1240 |                 </xs:element>
1241 |                 <xs:element name="ALIASES" minOccurs="0" maxOccurs="unbounded">
1242 |                     <xs:annotation>
1243 |                         <xs:documentation>This gets indexed.  Use this for alternate names, as for 1000 genomes.</xs:documentation>
1244 |                     </xs:annotation>
1245 |                     <xs:complexType>
1246 |                         <xs:attribute name="alias" use="required" type="xs:string"/>
1247 |                     </xs:complexType>
1248 |                 </xs:element>
1249 |                 <xs:element name="LINK" type="LinkType" minOccurs="0" maxOccurs="unbounded">
1250 |                     <xs:annotation>
1251 |                         <xs:documentation>generic study links</xs:documentation>
1252 |                     </xs:annotation>
1253 |                 </xs:element>
1254 |             </xs:sequence>
1255 |             <xs:attribute name="bioproject_accession" use="optional" type="xs:string">
1256 |                 <xs:annotation>
1257 |                     <xs:documentation>
1258 |                         BioProject accession (https://www.ncbi.nlm.nih.gov/bioproject)
1259 |                     </xs:documentation>
1260 |                 </xs:annotation>
1261 |             </xs:attribute>
1262 |             <xs:attribute name="study_url" use="optional" type="xs:anyURI">
1263 |                 <xs:annotation>
1264 |                     <xs:documentation>
1265 |                         Submitter location of data eg PI lab                       
1266 |                     </xs:documentation>
1267 |                 </xs:annotation>
1268 |             </xs:attribute>
1269 |     	    <xs:attribute name="study_url_invalid" type="xs:boolean">
1270 |                 <xs:annotation>
1271 |                     <xs:documentation>
1272 |                         Indicates the study URL is not valid.                    
1273 |                     </xs:documentation>
1274 |                 </xs:annotation>
1275 |             </xs:attribute>
1276 |             <xs:attribute name="dbGaP_id" use="optional" type="xs:string">
1277 |                 <xs:annotation>
1278 |                     <xs:documentation>
1279 |                         dbGaP identifier                       
1280 |                     </xs:documentation>
1281 |                 </xs:annotation>
1282 |             </xs:attribute>
1283 |             <xs:attribute name="ega_id" use="optional" type="xs:string">
1284 |                 <xs:annotation>
1285 |                     <xs:documentation>
1286 |                         EGA identifier                       
1287 |                     </xs:documentation>
1288 |                 </xs:annotation>
1289 |             </xs:attribute>
1290 |             <xs:attribute name="study_accession" use="optional" type="xs:string">
1291 |                 <xs:annotation>
1292 |                     <xs:documentation>
1293 |                         DDBJ/EBI/NCBI assigned accession for the study                                  
1294 |                     </xs:documentation>
1295 |                 </xs:annotation>
1296 |             </xs:attribute>
1297 |             <xs:attribute name="study_type" use="required" type="StudyTypeCV">
1298 |                 <xs:annotation>
1299 |                     <xs:documentation>                     
1300 |                     </xs:documentation>
1301 |                 </xs:annotation>
1302 |             </xs:attribute>
1303 |             <xs:attribute name="hold_date" use="optional" type="xs:date">
1304 |                 <xs:annotation>
1305 |                     <xs:documentation>
1306 |                         Date of scheduled release of data                         
1307 |                     </xs:documentation>
1308 |                 </xs:annotation>
1309 |             </xs:attribute>
1310 |             <xs:attribute name="is_indirect_submission" use="optional" type="xs:boolean">
1311 |                 <xs:annotation>
1312 |                     <xs:documentation>Enter 1 if this study was loaded by NCBI/EBI from historical data
1313 |                     </xs:documentation>
1314 |                 </xs:annotation>
1315 |             </xs:attribute>
1316 |             <xs:attribute name="dbGaP_release_date" use="optional" type="xs:date"/>
1317 |             <xs:attribute name="submitter_version" use="optional" type="xs:string">
1318 |                 <xs:annotation>
1319 |                     <xs:documentation>
1320 |                         When a study is updated and linked to an external data source (e.g. COSMIC) this attribute indicates the version/date of the external data source                         
1321 |                     </xs:documentation>
1322 |                 </xs:annotation>
1323 |             </xs:attribute>
1324 |             <xs:attribute name="last_updated_date" use="optional" type="xs:date">
1325 |                 <xs:annotation>
1326 |                     <xs:documentation>
1327 |                         For updating studies, the freeze date of the newly submitted data                         
1328 |                     </xs:documentation>
1329 |                 </xs:annotation>
1330 |             </xs:attribute>
1331 |             <xs:attribute name="is_curated" use="optional" type="xs:boolean">
1332 |                 <xs:annotation>
1333 |                     <xs:documentation>
1334 |                         Indicates the study is curated.                      
1335 |                     </xs:documentation>
1336 |                 </xs:annotation>
1337 |             </xs:attribute>
1338 |         </xs:complexType>
1339 |     </xs:element>
1340 | 
1341 |     <xs:element name="EXPERIMENT">
1342 |         <xs:annotation>
1343 |             <xs:documentation>
1344 |                 Details of methods used to generate raw data                                                        
1345 |             </xs:documentation>
1346 |         </xs:annotation>
1347 |         <xs:complexType>
1348 |             <xs:sequence>
1349 |                 <xs:element name="METHOD" minOccurs="1" maxOccurs="1">
1350 |                     <xs:annotation>
1351 |                         <xs:documentation>
1352 |                             Details of method used to generate data                                                        
1353 |                         </xs:documentation>
1354 |                     </xs:annotation>
1355 |                     <xs:complexType>
1356 |                         <xs:sequence>
1357 |                             <xs:element maxOccurs="1" minOccurs="0" name="DESCRIPTION"
1358 |                                 type="xs:string">
1359 |                                 <xs:annotation>
1360 |                                     <xs:documentation>
1361 |                                         Free text method description                                                      
1362 |                                     </xs:documentation>
1363 |                                 </xs:annotation>
1364 |                             </xs:element>
1365 |                         </xs:sequence>
1366 |                         <xs:attribute name="method_type" use="required" type="MethodTypeCV"/>
1367 |                     </xs:complexType>
1368 |                 </xs:element>
1369 |                 <xs:choice minOccurs="0">
1370 |                     <xs:element maxOccurs="1" minOccurs="1" name="DISCOVERY_ANALYSIS">
1371 |                         <xs:annotation>
1372 |                             <xs:documentation>
1373 | 								Analysis of the data provided by the method                                                   
1374 | 							</xs:documentation>
1375 |                         </xs:annotation>
1376 |                         <xs:complexType>
1377 |                             <xs:sequence>
1378 |                                 <xs:element maxOccurs="1" minOccurs="0" name="DESCRIPTION"
1379 |                                     type="xs:string">
1380 |                                     <xs:annotation>
1381 |                                         <xs:documentation>
1382 | 										Free text description of the analysis                                                   
1383 | 									</xs:documentation>
1384 |                                     </xs:annotation>
1385 |                                 </xs:element>
1386 |                             </xs:sequence>
1387 |                             <xs:attribute name="analysis_type" type="AnalysisTypeCV" use="required">
1388 |                                 <xs:annotation>
1389 |                                     <xs:documentation>
1390 | 									Analysis type, from AnalysisTypeCV                                                   
1391 | 								</xs:documentation>
1392 |                                 </xs:annotation>
1393 |                             </xs:attribute>
1394 |                             <xs:attribute name="reference_type" type="ReferenceTypeCV"
1395 |                                 use="required">
1396 |                                 <xs:annotation>
1397 |                                     <xs:documentation>
1398 | 	                	                Reference Type, from ReferenceTypeCV                                                  
1399 | 	                	            </xs:documentation>
1400 |                                 </xs:annotation>
1401 |                             </xs:attribute>
1402 |                             <xs:attribute name="reference_value" type="xs:string" use="required">
1403 |                                 <xs:annotation>
1404 |                                     <xs:documentation>
1405 | 	                	                Reference value                                                   
1406 | 	                	            </xs:documentation>
1407 |                                 </xs:annotation>
1408 |                             </xs:attribute>
1409 |                         </xs:complexType>
1410 |                     </xs:element>
1411 |                     <xs:element maxOccurs="1" minOccurs="1" name="VALIDATION_ANALYSIS">
1412 |                         <xs:annotation>
1413 |                             <xs:documentation>
1414 | 								Analysis of the data provided by the method                                                   
1415 | 							</xs:documentation>
1416 |                         </xs:annotation>
1417 |                         <xs:complexType>
1418 |                             <xs:sequence>
1419 |                                 <xs:element maxOccurs="1" minOccurs="0" name="DESCRIPTION"
1420 |                                     type="xs:string">
1421 |                                     <xs:annotation>
1422 |                                         <xs:documentation>
1423 | 										Free text description of the analysis                                                   
1424 | 									</xs:documentation>
1425 |                                     </xs:annotation>
1426 |                                 </xs:element>
1427 |                             </xs:sequence>
1428 |                             <xs:attribute name="analysis_type" type="AnalysisTypeCV" use="required">
1429 |                                 <xs:annotation>
1430 |                                     <xs:documentation>
1431 | 									Analysis type, from AnalysisTypeCV                                                   
1432 | 								</xs:documentation>
1433 |                                 </xs:annotation>
1434 |                             </xs:attribute>
1435 |                             <xs:attribute name="reference_type" type="ReferenceTypeCV"
1436 |                                 use="optional">
1437 |                                 <xs:annotation>
1438 |                                     <xs:documentation>
1439 | 	                	                Reference Type, from ReferenceTypeCV                                                  
1440 | 	                	            </xs:documentation>
1441 |                                 </xs:annotation>
1442 |                             </xs:attribute>
1443 |                             <xs:attribute name="reference_value" type="xs:string" use="optional">
1444 |                                 <xs:annotation>
1445 |                                     <xs:documentation>
1446 | 	                	                Reference value                                                   
1447 | 	                	            </xs:documentation>
1448 |                                 </xs:annotation>
1449 |                             </xs:attribute>
1450 |                         </xs:complexType>
1451 |                     </xs:element>
1452 |                     <xs:element maxOccurs="1" minOccurs="1" name="GENOTYPING_ANALYSIS">
1453 |                         <xs:annotation>
1454 |                             <xs:documentation>
1455 | 								Analysis of the data provided by the method                                                   
1456 | 							</xs:documentation>
1457 |                         </xs:annotation>
1458 |                         <xs:complexType>
1459 |                             <xs:sequence>
1460 |                                 <xs:element maxOccurs="1" minOccurs="0" name="DESCRIPTION"
1461 |                                     type="xs:string">
1462 |                                     <xs:annotation>
1463 |                                         <xs:documentation>
1464 | 										Free text description of the analysis                                                   
1465 | 									</xs:documentation>
1466 |                                     </xs:annotation>
1467 |                                 </xs:element>
1468 |                             </xs:sequence>
1469 |                             <xs:attribute name="analysis_type" type="AnalysisTypeCV" use="required">
1470 |                                 <xs:annotation>
1471 |                                     <xs:documentation>
1472 | 									Analysis type, from AnalysisTypeCV                                                   
1473 | 								</xs:documentation>
1474 |                                 </xs:annotation>
1475 |                             </xs:attribute>
1476 |                             <xs:attribute name="reference_type" type="ReferenceTypeCV"
1477 |                                 use="optional">
1478 |                                 <xs:annotation>
1479 |                                     <xs:documentation>
1480 | 	                	                Reference Type, from ReferenceTypeCV                                                  
1481 | 	                	            </xs:documentation>
1482 |                                 </xs:annotation>
1483 |                             </xs:attribute>
1484 |                             <xs:attribute name="reference_value" type="xs:string" use="optional">
1485 |                                 <xs:annotation>
1486 |                                     <xs:documentation>
1487 | 	                	                Reference value                                                   
1488 | 	                	            </xs:documentation>
1489 |                                 </xs:annotation>
1490 |                             </xs:attribute>
1491 |                         </xs:complexType>
1492 |                     </xs:element>
1493 |                 </xs:choice>
1494 |                 <xs:element name="DETECTION" minOccurs="0">
1495 |                     <xs:complexType>
1496 |                         <xs:sequence>
1497 |                             <xs:element name="DESCRIPTION" type="xs:string" minOccurs="0"
1498 |                                 maxOccurs="1">
1499 |                                 <xs:annotation>
1500 |                                     <xs:documentation>Details of software/algorithm parameters used </xs:documentation>
1501 |                                 </xs:annotation>
1502 |                             </xs:element>
1503 |                         </xs:sequence>
1504 |                         <xs:attribute name="detection_method" use="optional" type="xs:string">
1505 |                             <xs:annotation>
1506 |                                 <xs:documentation>
1507 |                                     Short description or keywords for software/algorithm(s) used eg ADM2, Birdsuite, BrkPtr, CNVFinder                      
1508 |                                 </xs:documentation>
1509 |                             </xs:annotation>
1510 |                         </xs:attribute>
1511 |                     </xs:complexType>
1512 |                 </xs:element>
1513 |                 <xs:element name="PLATFORM" minOccurs="0" maxOccurs="unbounded">
1514 |                     <xs:complexType>
1515 |                         <xs:sequence>
1516 |                             <xs:element name="LINK" type="LinkType" minOccurs="0"
1517 |                                 maxOccurs="unbounded">
1518 |                                 <xs:annotation>
1519 |                                     <xs:documentation>Platform links.</xs:documentation>
1520 |                                 </xs:annotation>
1521 |                             </xs:element>
1522 |                         </xs:sequence>
1523 |                         <xs:attribute name="platform_name" use="optional" type="xs:string">
1524 |                             <xs:annotation>
1525 |                                 <xs:documentation>
1526 |                                     Name of  sequencing platform eg Capillary, 454, Helicos, Solexa, SOLiD or name of array platform if not in GEO or Array Express                                               
1527 |                                 </xs:documentation>
1528 |                             </xs:annotation>
1529 |                         </xs:attribute>
1530 |                     </xs:complexType>
1531 |                 </xs:element>
1532 |                 <xs:element name="LINK" maxOccurs="unbounded" minOccurs="0">
1533 |                     <xs:complexType>
1534 |                         <xs:choice>
1535 |                             <xs:element name="DB_ID" type="LinkType" minOccurs="1" maxOccurs="1"/>
1536 |                             <xs:element name="URL" type="URLType" minOccurs="1" maxOccurs="1"/>
1537 |                         </xs:choice>
1538 |                     </xs:complexType>
1539 |                 </xs:element>
1540 |                 <xs:element name="LIBRARY" type="LibraryType" minOccurs="0" maxOccurs="unbounded"/>
1541 |                 <xs:element name="CURATION" minOccurs="0" maxOccurs="1">
1542 |                     <xs:annotation>
1543 |                         <xs:documentation>
1544 |                             Details of curation by DDBJ/EBI/NCBI, if this has occurred
1545 | 		        </xs:documentation>
1546 |                     </xs:annotation>
1547 |                     <xs:complexType>
1548 |                         <xs:attribute name="curator_name" use="required" type="xs:string"/>
1549 |                         <xs:attribute name="curator_email" use="required" type="xs:string"/>
1550 |                         <xs:attribute name="curated_set_name" use="optional" type="xs:string"/>
1551 |                         <xs:attribute name="curated_set_link" use="optional" type="xs:anyURI"/>
1552 |                     </xs:complexType>
1553 |                 </xs:element>
1554 |                 <xs:element name="MERGED_EXPERIMENT" minOccurs="0" maxOccurs="unbounded">
1555 |                     <xs:annotation>
1556 |                         <xs:documentation>
1557 |                             IDs of experiments merged to make this one                                                  
1558 |                         </xs:documentation>
1559 |                     </xs:annotation>
1560 |                     <xs:complexType>
1561 |                         <xs:attribute name="merged_experiment_id" use="required"
1562 |                             type="xs:positiveInteger"/>
1563 |                     </xs:complexType>
1564 |                 </xs:element>
1565 |             </xs:sequence>
1566 |             <xs:attribute name="experiment_id" use="required" type="xs:positiveInteger">
1567 |                 <xs:annotation>
1568 |                     <xs:documentation>
1569 |                         id of the experiment supplied by submitter                        
1570 |                     </xs:documentation>
1571 |                 </xs:annotation>
1572 |             </xs:attribute>
1573 |             <xs:attribute name="sra_accession" use="optional" type="xs:string">
1574 |                 <xs:annotation>
1575 |                     <xs:documentation>
1576 |                         SRA Experiment accession (https://www.ncbi.nlm.nih.gov/books/NBK47529/#_SRA_Quick_Sub_BK_Experiment_)
1577 |                     </xs:documentation>
1578 |                 </xs:annotation>
1579 |             </xs:attribute>
1580 |             <xs:attribute name="experiment_type" use="optional" type="ExperimentTypeCV"/>
1581 |             <xs:attribute name="site" type="xs:string">
1582 |                 <xs:annotation>
1583 |                     <xs:documentation>For multicenter studies, the location where the experiment took place</xs:documentation>
1584 |                 </xs:annotation>
1585 |             </xs:attribute>
1586 |             <xs:attribute name="experiment_resolution" use="optional" type="xs:string">
1587 |                 <xs:annotation>
1588 |                     <xs:documentation>
1589 |                                     Estimate of the resolution (kb)                        
1590 |                                 </xs:documentation>
1591 |                 </xs:annotation>
1592 |             </xs:attribute>
1593 |         </xs:complexType>
1594 |     </xs:element>
1595 | 
1596 |     <xs:element name="SAMPLESET">
1597 |         <xs:annotation>
1598 |             <xs:documentation>
1599 |                 Details of each sampleset/population used in the study                       
1600 |             </xs:documentation>
1601 |         </xs:annotation>
1602 |         <xs:complexType>
1603 |             <xs:sequence>
1604 |                 <xs:element name="DESCRIPTION" type="xs:string" minOccurs="0" maxOccurs="1"/>
1605 |                 <xs:element name="ORGANISM" minOccurs="1" maxOccurs="unbounded">
1606 |                     <xs:complexType>
1607 |                         <xs:attribute name="taxonomy_id" use="required" type="xs:positiveInteger">
1608 |                             <xs:annotation>
1609 |                                 <xs:documentation>
1610 |                                     NCBI Taxonomy ID (https://www.ncbi.nlm.nih.gov/taxonomy)                                 
1611 |                                 </xs:documentation>
1612 |                             </xs:annotation>
1613 |                         </xs:attribute>
1614 |                     </xs:complexType>
1615 |                 </xs:element>
1616 |                 <xs:element name="PHENOTYPE" maxOccurs="1" minOccurs="0" type="PhenotypeType"
1617 |                     form="unqualified"/>
1618 |             </xs:sequence>
1619 |             <xs:attribute name="sampleset_id" use="required" type="xs:positiveInteger">
1620 |                 <xs:annotation>
1621 |                     <xs:documentation>
1622 |                         Sampleset ID supplied by submitter                  
1623 |                     </xs:documentation>
1624 |                 </xs:annotation>
1625 |             </xs:attribute>
1626 |             <xs:attribute name="sampleset_name" use="optional" type="xs:string">
1627 |                 <xs:annotation>
1628 |                     <xs:documentation>
1629 |                         Submitter defined sampleset  name                       
1630 |                     </xs:documentation>
1631 |                 </xs:annotation>
1632 |             </xs:attribute>
1633 |             <xs:attribute name="sampleset_size" use="required" type="xs:nonNegativeInteger">
1634 |                 <xs:annotation>
1635 |                     <xs:documentation>
1636 |                         Number of samples in sampleset                        
1637 |                     </xs:documentation>
1638 |                 </xs:annotation>
1639 |             </xs:attribute>
1640 |             <xs:attribute name="sampleset_type" type="SamplesetTypeCV" use="optional"> </xs:attribute>
1641 |             <xs:attribute name="sampleset_sex" use="optional" type="SexCV"/>
1642 |             <xs:attribute name="sampleset_population" use="optional" type="xs:string">
1643 |                 <xs:annotation>
1644 |                     <xs:documentation>            
1645 |                         Population of the sampleset                        
1646 |                     </xs:documentation>
1647 |                 </xs:annotation>
1648 |             </xs:attribute>
1649 |         </xs:complexType>
1650 |     </xs:element>
1651 | 
1652 |     <xs:element name="SAMPLE">
1653 |         <xs:annotation>
1654 |             <xs:documentation>
1655 |                 Details of each sample used in the study                
1656 |             </xs:documentation>
1657 |         </xs:annotation>
1658 |         <xs:complexType>
1659 |             <xs:sequence>
1660 |                 <xs:element name="SAMPLESET" minOccurs="0" maxOccurs="unbounded">
1661 |                     <xs:complexType>
1662 |                         <xs:attribute name="sampleset_id" type="xs:positiveInteger" use="required">
1663 |                             <xs:annotation>
1664 |                                 <xs:documentation>
1665 |                                     Sample sampleset_id                           
1666 |                                 </xs:documentation>
1667 |                             </xs:annotation>
1668 |                         </xs:attribute>
1669 |                     </xs:complexType>
1670 |                 </xs:element>
1671 |                 <xs:element name="LINK" maxOccurs="unbounded" minOccurs="0" type="LinkType">
1672 |                     <xs:annotation>
1673 |                         <xs:documentation>
1674 |                             If sample information has been deposited to a samples database (e.g. BioSD), or is commercially available (e.g. from the Jackson Laboratory) provide the details                                       
1675 |                         </xs:documentation>
1676 |                     </xs:annotation>
1677 |                 </xs:element>
1678 |             </xs:sequence>
1679 |             <xs:attribute name="sample_id" use="required" type="xs:string">
1680 |                 <xs:annotation>
1681 |                     <xs:documentation>
1682 |                         Sample ID supplied by submitter                        
1683 |                     </xs:documentation>
1684 |                 </xs:annotation>
1685 |             </xs:attribute>
1686 |             <xs:attribute name="sample_cell_type" use="optional" type="xs:string">
1687 |                 <xs:annotation>
1688 |                     <xs:documentation>
1689 |                         Cell/tissue type from which the sample was obtained                    
1690 |                     </xs:documentation>
1691 |                 </xs:annotation>
1692 |             </xs:attribute>
1693 |             <xs:attribute name="subject_id" use="required" type="xs:string">
1694 |                 <xs:annotation>
1695 |                     <xs:documentation>
1696 |                         Reference to subject ID supplied by submitter                        
1697 |                     </xs:documentation>
1698 |                 </xs:annotation>
1699 |             </xs:attribute>
1700 |             <xs:attribute name="sample_attribute" type="xs:string">
1701 |                 <xs:annotation>
1702 |                     <xs:documentation>cancer, histology, toxicology,...</xs:documentation>
1703 |                 </xs:annotation>
1704 |             </xs:attribute>
1705 |             <xs:attribute name="sample_cancer" use="optional" type="xs:boolean">
1706 |                 <xs:annotation>
1707 |                     <xs:documentation>
1708 |                         1 if sample was derived from cancerous cells or tissue                   
1709 |                     </xs:documentation>
1710 |                 </xs:annotation>
1711 |             </xs:attribute>
1712 |             <xs:attribute name="sample_karyotype" use="optional" type="xs:string">
1713 |                 <xs:annotation>
1714 |                     <xs:documentation>            
1715 |                         The sample's karyotype in ISCN notation, e.g. 47,XXY or 46,XY,t(12;16)(q13;p11)  
1716 |                     </xs:documentation>
1717 |                 </xs:annotation>
1718 |             </xs:attribute>
1719 |             <xs:attribute name="biosample_accession" use="optional" type="xs:string">
1720 |                 <xs:annotation>
1721 |                     <xs:documentation>            
1722 |                         Sample accession from DDBJ/EBI/NCBI BioSample
1723 |                     </xs:documentation>
1724 |                 </xs:annotation>
1725 |             </xs:attribute>
1726 |         </xs:complexType>
1727 |     </xs:element>
1728 | 
1729 |     <xs:element name="SUBJECT">
1730 |         <xs:annotation>
1731 |             <xs:documentation>
1732 |                 Details of each subject/individual used in the study                
1733 |             </xs:documentation>
1734 |         </xs:annotation>
1735 |         <xs:complexType>
1736 |             <xs:sequence>
1737 |                 <xs:element name="PHENOTYPE" maxOccurs="1" minOccurs="0" type="PhenotypeType"/>
1738 |             </xs:sequence>
1739 |             <xs:attribute name="subject_id" use="required" type="xs:string">
1740 |                 <xs:annotation>
1741 |                     <xs:documentation>
1742 |                         Subject ID supplied by submitter                                
1743 |                     </xs:documentation>
1744 |                 </xs:annotation>
1745 |             </xs:attribute>
1746 |             <xs:attribute name="subject_taxonomy_id" use="required" type="xs:positiveInteger">
1747 |                 <xs:annotation>
1748 |                     <xs:documentation>
1749 |                         NCBI tax ID  (https://www.ncbi.nlm.nih.gov/taxonomy)                              
1750 |                     </xs:documentation>
1751 |                 </xs:annotation>
1752 |             </xs:attribute>
1753 |             <xs:attribute name="subject_maternal_id" use="optional" type="xs:string">
1754 |                 <xs:annotation>
1755 |                     <xs:documentation>
1756 |                         Reference to maternal Subject ID           
1757 |                     </xs:documentation>
1758 |                 </xs:annotation>
1759 |             </xs:attribute>
1760 |             <xs:attribute name="subject_paternal_id" use="optional" type="xs:string">
1761 |                 <xs:annotation>
1762 |                     <xs:documentation>
1763 |                         Reference to paternal Subject ID                   
1764 |                     </xs:documentation>
1765 |                 </xs:annotation>
1766 |             </xs:attribute>
1767 |             <xs:attribute name="subject_sex" use="optional" type="SexCV"/>
1768 |             <xs:attribute name="subject_collection" use="optional" type="CollectionCV">
1769 |                 <xs:annotation>
1770 |                     <xs:documentation>            
1771 |                           Indicates if the subject is included in either the International HapMap Project (HapMap) or Human Genome Diversity Project (HGDP)                   
1772 |                      </xs:documentation>
1773 |                 </xs:annotation>
1774 |             </xs:attribute>
1775 |             <xs:attribute name="subject_karyotype" use="optional" type="xs:string">
1776 |                 <xs:annotation>
1777 |                     <xs:documentation>            
1778 |                           The subject's karyotype in ISCN notation, e.g. 47,XXY or 46,XY,t(12;16)(q13;p11)  
1779 |                      </xs:documentation>
1780 |                 </xs:annotation>
1781 |             </xs:attribute>
1782 |             <xs:attribute name="subject_population" use="optional" type="xs:string">
1783 |                 <xs:annotation>
1784 |                     <xs:documentation>
1785 |                         Free-form subject ethnicity as defined by submitter                                             
1786 |                     </xs:documentation>
1787 |                 </xs:annotation>
1788 |             </xs:attribute>
1789 |             <xs:attribute name="subject_age" use="optional" type="positive-decimal">
1790 |                 <xs:annotation>
1791 |                     <xs:documentation>            
1792 |                         The subject's age                        
1793 |                     </xs:documentation>
1794 |                 </xs:annotation>
1795 |             </xs:attribute>
1796 |             <xs:attribute name="subject_age_units" use="optional" type="SubjectAgeUnitsCV">
1797 |                 <xs:annotation>
1798 |                     <xs:documentation>            
1799 |                         The subject's age units                       
1800 |                     </xs:documentation>
1801 |                 </xs:annotation>
1802 |             </xs:attribute>
1803 |         </xs:complexType>
1804 |     </xs:element>
1805 | 
1806 |     <xs:element name="VARIANT_CALL">
1807 |         <xs:annotation>
1808 |             <xs:documentation>
1809 |             Details of each variant call identified in the study        
1810 |         </xs:documentation>
1811 |         </xs:annotation>
1812 |         <xs:complexType>
1813 |             <xs:sequence>
1814 |                 <xs:element name="VALIDATION" minOccurs="0" maxOccurs="unbounded">
1815 |                     <xs:complexType>
1816 |                         <xs:attribute name="experiment_id" use="required" type="xs:positiveInteger"/>
1817 |                         <xs:attribute name="result" use="required" type="ValidationResultCV"/>
1818 |                     </xs:complexType>
1819 |                 </xs:element>
1820 |                 <xs:element name="DESCRIPTION" maxOccurs="1" minOccurs="0" type="xs:string">
1821 |                     <xs:annotation>
1822 |                         <xs:documentation>Free-form description of variant</xs:documentation>
1823 |                     </xs:annotation>
1824 |                 </xs:element>
1825 |                 <xs:choice>
1826 |                     <xs:element name="SAMPLE" maxOccurs="1" minOccurs="1">
1827 |                         <xs:complexType>
1828 |                             <xs:attribute name="sample_id" use="required" type="xs:string">
1829 |                                 <xs:annotation>
1830 |                                     <xs:documentation>
1831 |                                         References SAMPLE/sample_id.                         
1832 |                                     </xs:documentation>
1833 |                                 </xs:annotation>
1834 |                             </xs:attribute>
1835 |                         </xs:complexType>
1836 |                     </xs:element>
1837 |                     <xs:element name="SAMPLESET" maxOccurs="1" minOccurs="1">
1838 |                         <xs:complexType>
1839 |                             <xs:attribute name="sampleset_id" use="required"
1840 |                                 type="xs:positiveInteger">
1841 |                                 <xs:annotation>
1842 |                                     <xs:documentation>
1843 |                                         References SAMPLESET/sampleset_id.                         
1844 |                                     </xs:documentation>
1845 |                                 </xs:annotation>
1846 |                             </xs:attribute>
1847 |                         </xs:complexType>
1848 |                     </xs:element>
1849 |                 </xs:choice>
1850 |                 <xs:element name="LINK" type="LinkType" minOccurs="0" maxOccurs="unbounded"/>
1851 |                 <xs:element name="PHENOTYPE" maxOccurs="1" minOccurs="0" type="PhenotypeType"/>
1852 |                 <xs:element name="PLACEMENT" maxOccurs="unbounded" minOccurs="0"
1853 |                     type="CallPlacementType"> </xs:element>
1854 |                 <xs:element name="VARIANT_SEQUENCE" type="xs:string" minOccurs="0">
1855 |                     <xs:annotation>
1856 |                         <xs:documentation>raw sequence eg ATGTTAA/atgttaa of inserted or replacement sequence </xs:documentation>
1857 |                     </xs:annotation>
1858 |                 </xs:element>
1859 |                 <xs:element name="SUPPORT" maxOccurs="unbounded" minOccurs="0" type="SeqType">
1860 |                     <xs:annotation>
1861 |                         <xs:documentation>Evidence or Support sequences</xs:documentation>
1862 |                     </xs:annotation>
1863 |                 </xs:element>
1864 |             </xs:sequence>
1865 |             <xs:attribute name="variant_call_id" type="xs:string" use="required">
1866 |                 <xs:annotation>
1867 |                     <xs:documentation>
1868 |                         Submitter id of the VARIANT_CALL             
1869 |                     </xs:documentation>
1870 |                 </xs:annotation>
1871 |             </xs:attribute>
1872 |             <xs:attribute name="variant_call_accession" use="optional" type="xs:string">
1873 |                 <xs:annotation>
1874 |                     <xs:documentation>DDBJ/EBI/NCBI assigned accession of the variant call</xs:documentation>
1875 |                 </xs:annotation>
1876 |             </xs:attribute>
1877 |             <xs:attribute name="variant_call_type" type="VariantCallTypeCV" use="required"/>
1878 |             <xs:attribute name="variant_call_type_SO_id" type="xs:string"/>
1879 |             <xs:attribute name="clinical_source" type="xs:string">
1880 |                 <xs:annotation>
1881 |                     <xs:documentation>Source of Clinical Significance: ClinVar, Submitter, ClinGen Dosage Sensitivity Map</xs:documentation>
1882 |                 </xs:annotation>
1883 |             </xs:attribute>
1884 |             <xs:attribute name="clinical_significance" type="xs:string">
1885 |                 <xs:annotation>
1886 |                     <xs:documentation>
1887 |                         Studies with clinical_significance should be submitted directly to ClinVar. 
1888 |                         There are still some legacy studies with clinical_significance, including ClinGen.
1889 |                         Changed from ClinicalSignificanceCV to string to allow types from ClinVar aggregated at the region level.
1890 |                     </xs:documentation>
1891 |                 </xs:annotation>
1892 |             </xs:attribute>
1893 |             <xs:attribute name="insertion_length" use="optional" type="xs:string">
1894 |                 <xs:annotation>
1895 |                     <xs:documentation>If this call is an insertion of any kind, this field indicates the length of the inserted sequence, and is required (value may be approximate, e.g., "150-300"). Can also be used for a mapping-based deletion, to indicate the approximate size of the deleted sequence.
1896 |                     </xs:documentation>
1897 |                 </xs:annotation>
1898 |             </xs:attribute>
1899 |             <xs:attribute name="zygosity" type="VariantCallZygosityCV"/>
1900 |             <xs:attribute name="origin" type="OriginCV"/>
1901 |             <xs:attribute name="copy_number" type="xs:string">
1902 |                 <xs:annotation>
1903 |                     <xs:documentation>
1904 |                         Needs to be a string to support values like "4+".                                               
1905 |                     </xs:documentation>
1906 |                 </xs:annotation>
1907 |             </xs:attribute>
1908 |             <xs:attribute name="reference_copy_number" type="xs:string">
1909 |                 <xs:annotation>
1910 |                     <xs:documentation>Indicates the expected copy number for this variant in the default state.</xs:documentation>
1911 |                 </xs:annotation>
1912 |             </xs:attribute>
1913 |             <xs:attribute name="support_count" type="xs:positiveInteger" use="optional">
1914 |                 <xs:annotation>
1915 |                     <xs:documentation>
1916 |                         Number of variant probes or clones                                               
1917 |                     </xs:documentation>
1918 |                 </xs:annotation>
1919 |             </xs:attribute>
1920 |             <xs:attribute name="log2_value" type="xs:float" use="optional">
1921 |                 <xs:annotation>
1922 |                     <xs:documentation>
1923 |                         Average log2 ratio for variant probes                                               
1924 |                     </xs:documentation>
1925 |                 </xs:annotation>
1926 |             </xs:attribute>
1927 |             <xs:attribute name="is_low_quality" type="xs:boolean" use="optional">
1928 |                 <xs:annotation>
1929 |                     <xs:documentation>
1930 |                         1/true indicates low-quality data, as in some variants in 1000 genomes project (used for filtering)                                              
1931 |                     </xs:documentation>
1932 |                 </xs:annotation>
1933 |             </xs:attribute>
1934 |             <xs:attribute name="experiment_id" use="required" type="xs:positiveInteger"/>
1935 |             <xs:attribute name="allele_count" type="xs:nonNegativeInteger">
1936 |                 <xs:annotation>
1937 |                     <xs:documentation>From 1000 Genomes VCF spec: AC : allele count in genotypes, for each ALT allele, in the same order as listed
1938 |                         </xs:documentation>
1939 |                 </xs:annotation>
1940 |             </xs:attribute>
1941 |             <xs:attribute name="allele_frequency" type="xs:string">
1942 |                 <xs:annotation>
1943 |                     <xs:documentation>From 1000 Genomes VCF spec: AF : allele frequency for each ALT allele in the same order as listed: use this when estimated from primary 
1944 |                         </xs:documentation>
1945 |                 </xs:annotation>
1946 |             </xs:attribute>
1947 |             <xs:attribute name="allele_number" type="xs:nonNegativeInteger">
1948 |                 <xs:annotation>
1949 |                     <xs:documentation>From 1000 Genomes VCF spec: AN : total number of alleles in called genotypes
1950 |                         </xs:documentation>
1951 |                 </xs:annotation>
1952 |             </xs:attribute>
1953 |             <xs:attribute name="repeat_count" type="xs:string">
1954 |                 <xs:annotation>
1955 |                     <xs:documentation>Use for short tandem repeat. Combine repeat motif, repeat count, and optional indication if this is the reference allele. Example: "[TG]12.5 (ref)".
1956 |                         </xs:documentation>
1957 |                 </xs:annotation>
1958 |             </xs:attribute>
1959 |         </xs:complexType>
1960 |     </xs:element>
1961 | 
1962 |     <xs:element name="VARIANT_REGION">
1963 |         <xs:annotation>
1964 |             <xs:documentation>
1965 |                 Details of each variant region identified in the study        
1966 |             </xs:documentation>
1967 |         </xs:annotation>
1968 |         <xs:complexType>
1969 |             <xs:sequence>
1970 |                 <xs:element name="DESCRIPTION" maxOccurs="1" minOccurs="0" type="xs:string">
1971 |                     <xs:annotation>
1972 |                         <xs:documentation>Free-form description of variant</xs:documentation>
1973 |                     </xs:annotation>
1974 |                 </xs:element>
1975 |                 <xs:element name="SUPPORTING_VARIANT_CALL" maxOccurs="unbounded" minOccurs="0">
1976 |                     <xs:annotation>
1977 |                         <xs:documentation>Variant Calls that were merged into this region.</xs:documentation>
1978 |                     </xs:annotation>
1979 |                     <xs:complexType>
1980 |                         <xs:attribute name="variant_call_id" type="xs:string" use="required"/>
1981 |                         <xs:attribute name="mutation_order" use="optional" type="xs:positiveInteger"/>
1982 |                         <xs:attribute name="mutation_molecule" use="optional" type="xs:string"/>
1983 |                     </xs:complexType>
1984 |                 </xs:element>
1985 |                 <xs:element name="SUPPORTING_VARIANT_REGION" maxOccurs="unbounded" minOccurs="0">
1986 |                     <xs:annotation>
1987 |                         <xs:documentation>Variant Regions that were merged into this region.</xs:documentation>
1988 |                     </xs:annotation>
1989 |                     <xs:complexType>
1990 |                         <xs:attribute name="variant_region_id" type="xs:string" use="required"/>
1991 |                     </xs:complexType>
1992 |                 </xs:element>
1993 |                 <xs:element name="PLACEMENT" maxOccurs="unbounded" minOccurs="0"
1994 |                     type="RegionPlacementType"> </xs:element>
1995 |             </xs:sequence>
1996 |             <xs:attribute name="variant_region_id" use="required" type="xs:string">
1997 |                 <xs:annotation>
1998 |                     <xs:documentation>The submitter defined id of the VARIANT_REGION</xs:documentation>
1999 |                 </xs:annotation>
2000 |             </xs:attribute>
2001 |             <xs:attribute name="variant_region_accession" use="optional" type="xs:string">
2002 |                 <xs:annotation>
2003 |                     <xs:documentation>DDBJ/EBI/NCBI assigned accession of the variant region
2004 |                     </xs:documentation>
2005 |                 </xs:annotation>
2006 |             </xs:attribute>
2007 |             <xs:attribute name="assertion_method" use="required" type="xs:string">
2008 |                 <xs:annotation>
2009 |                     <xs:documentation>The assertion method used to assert the variant region</xs:documentation>
2010 |                 </xs:annotation>
2011 |             </xs:attribute>
2012 |             <xs:attribute name="variant_region_type" type="VariantRegionTypeCV" use="required"/>
2013 |             <xs:attribute name="variant_region_type_SO_id" type="xs:string"/>
2014 |             <xs:attribute name="is_low_quality" type="xs:boolean" use="optional">
2015 |                 <xs:annotation>
2016 |                     <xs:documentation>
2017 |                         1/true indicates low-quality data, as in some variants in 1000 genomes project (used for filtering)                                              
2018 |                     </xs:documentation>
2019 |                 </xs:annotation>
2020 |             </xs:attribute>
2021 |             <xs:attribute name="repeat_motif" type="xs:string">
2022 |                 <xs:annotation>
2023 |                     <xs:documentation>Use for short tandem repeat. Repeat motif, for example: "TG".
2024 |                         </xs:documentation>
2025 |                 </xs:annotation>
2026 |             </xs:attribute>
2027 |             <xs:attribute name="repeat_counts" type="xs:string">
2028 |                 <xs:annotation>
2029 |                     <xs:documentation>Use for short tandem repeat. Sorted list of repeat counts for reference and alternates.  For example: "13.5,14.5,15.5,16.5,17.5,18.5,19.5,20.5,21.5,22.5,23.5,26.5".
2030 |                         </xs:documentation>
2031 |                 </xs:annotation>
2032 |             </xs:attribute>
2033 |         </xs:complexType>
2034 |     </xs:element>
2035 | 
2036 |     <xs:element name="GENOTYPE">
2037 |         <xs:complexType>
2038 |             <xs:sequence>
2039 |                 <xs:choice>
2040 |                     <xs:element name="SAMPLE" maxOccurs="1">
2041 |                         <xs:complexType>
2042 |                             <xs:attribute name="sample_id" use="required" type="xs:string">
2043 |                                 <xs:annotation>
2044 |                                     <xs:documentation>
2045 |                                         Internal sample id              
2046 |                                     </xs:documentation>
2047 |                                 </xs:annotation>
2048 |                             </xs:attribute>
2049 |                         </xs:complexType>
2050 |                     </xs:element>
2051 |                     <xs:element name="SAMPLESET" maxOccurs="1">
2052 |                         <xs:complexType>
2053 |                             <xs:attribute name="sampleset_id" use="required"
2054 |                                 type="xs:positiveInteger">
2055 |                                 <xs:annotation>
2056 |                                     <xs:documentation>
2057 |                                         Internal sampleset id              
2058 |                                     </xs:documentation>
2059 |                                 </xs:annotation>
2060 |                             </xs:attribute>
2061 |                         </xs:complexType>
2062 |                     </xs:element>
2063 |                 </xs:choice>
2064 |                 <xs:element name="ALLELE" minOccurs="0" maxOccurs="unbounded">
2065 |                     <xs:complexType>
2066 |                         <xs:attribute name="reference_allele_type" use="optional" type="xs:string"/>
2067 |                         <xs:attribute name="alternate_allele_type" use="optional" type="xs:string"/>
2068 |                         <xs:attribute name="alternate_allele_code" use="optional" type="xs:string"/>
2069 |                         <xs:attribute name="presence" use="optional" type="xs:string"/>
2070 |                         <xs:attribute name="allele_copy_number" use="optional"
2071 |                             type="xs:nonNegativeInteger"/>
2072 |                         <xs:attribute name="inheritance" use="optional" type="xs:string"/>
2073 |                         <xs:attribute name="ancestral" use="optional" type="xs:boolean">
2074 |                             <xs:annotation>
2075 |                                 <xs:documentation>
2076 |                                     1=ancestral allele, 0=non-ancestral allele
2077 |                                 </xs:documentation>
2078 |                             </xs:annotation>
2079 |                         </xs:attribute>
2080 |                     </xs:complexType>
2081 |                 </xs:element>
2082 |             </xs:sequence>
2083 |             <xs:attribute name="variant_accession" use="required" type="xs:string"/>
2084 |             <xs:attribute name="success" use="required" type="xs:boolean"/>
2085 |             <xs:attribute name="submitted_genotype" use="optional" type="xs:string">
2086 |                 <xs:annotation>
2087 |                     <xs:documentation>
2088 |                         Submitted genotype 0|1, 0/1 etc. Where '|' is phased and '/' is unphased, and the digits refer to the alternate allele code for this genotype               
2089 |                     </xs:documentation>
2090 |                 </xs:annotation>
2091 |             </xs:attribute>
2092 |             <xs:attribute name="genotype_zygosity" use="optional" type="xs:string">
2093 |                 <xs:annotation>
2094 |                     <xs:documentation>
2095 |                         Submitted genotype eg heterozygous, hemizygous, haploid                 
2096 |                     </xs:documentation>
2097 |                 </xs:annotation>
2098 |             </xs:attribute>
2099 |             <xs:attribute name="absolute_copy_number" use="optional" type="xs:nonNegativeInteger"/>
2100 |             <xs:attribute name="experiment_id" use="required" type="xs:positiveInteger"/>
2101 |         </xs:complexType>
2102 |     </xs:element>
2103 | 
2104 |     <xs:element name="DELETED_VARIANTS">
2105 |         <xs:annotation>
2106 |             <xs:documentation>
2107 |                 List of dbVar accessions to be deleted
2108 |             </xs:documentation>
2109 |         </xs:annotation>
2110 |         <xs:complexType>
2111 |             <xs:attribute name="accession" use="required" type="xs:string">
2112 |                 <xs:annotation>
2113 |                     <xs:documentation>
2114 |                         dbVar sv accession                        
2115 |                     </xs:documentation>
2116 |                 </xs:annotation>
2117 |             </xs:attribute>
2118 |         </xs:complexType>
2119 |     </xs:element>
2120 | </xs:schema>
2121 | 


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/specs/dbVarSubmissionTemplate_v3.5.xlsx:
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/tutorials/README.md:
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1 | # dbVar Tutorials
2 | 
3 | ## Tutorials for NR data:
4 | https://github.com/ncbi/dbvar/blob/master/Structural_Variant_Sets/Nonredundant_Structural_Variants/ToolGuide.md
5 | 


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