├── .gitattributes ├── .gitignore ├── CAFE_pipeline_conda.yml ├── LICENSE ├── README.md ├── Variant_Catalogue_v1.sh ├── install.sh ├── main.nf ├── modules ├── GLnexus.nf ├── Hail_MEI_QC.nf ├── Hail_MEI_QC.py ├── Hail_STR.nf ├── Hail_STR.py ├── Hail_SV_QC.nf ├── Hail_SV_QC.py ├── Hail_sample_QC.nf ├── Hail_sample_QC.py ├── Hail_variant_MT_QC.nf ├── Hail_variant_MT_QC.py ├── Hail_variant_QC.nf ├── Hail_variant_QC.py ├── MEI_data_organization.R ├── MEI_data_organization.nf ├── MT_Extract_MT_Read.nf ├── MT_FilterOut_sites.nf ├── MT_Filter_Mutect_Calls.nf ├── MT_LeftAlignAndTrimVariants.nf ├── MT_Liftover.nf ├── MT_MarkDuplicates.nf ├── MT_MarkDuplicates_index.nf ├── MT_MergeVcfs.nf ├── MT_Merge_stat_file.nf ├── MT_Picard_CollectWgsMetrics_MT.nf ├── MT_SamtoFastq.nf ├── MT_Step1_input_tsv.nf ├── MT_Step2_participant_data.nf ├── MT_Step3_metadata.nf ├── MT_Step3_metadata_sample.R ├── MT_Step3_metadata_sample.nf ├── MT_align_to_MT.nf ├── MT_call_variants.nf ├── MT_data_organization.R ├── MT_data_organization.nf ├── MT_haplocheck.nf ├── MT_norm.nf ├── Picard_CollectAlignmentSummaryMetrics.nf ├── Picard_CollectWgsMetrics.nf ├── Picard_QualityScoreDistribution.nf ├── SNV_data_organization.R ├── SNV_data_organization.nf ├── STR_data_organization.R ├── STR_data_organization.nf ├── SV_concat_by_sample.nf ├── SV_data_organization.R ├── SV_data_organization.nf ├── SV_jasmine.nf ├── SV_manta.nf ├── SV_paragraph_duphold.nf ├── SV_smoove.nf ├── align_sort_output_bam.nf ├── annotation_table_merged.nf ├── annotation_table_merged_no_snv.nf ├── archive │ ├── Bcftools_stats.nf │ ├── GATK_index.nf │ ├── Hail.nf │ ├── Hail_variant_QC_220512.py │ ├── MT_merge_samples.nf │ ├── MT_vcfs_txt.nf │ ├── QC_indiv.nf │ ├── SNV_data_organization.R │ ├── SNV_data_organization.nf │ ├── SNV_data_organization_220504.R │ ├── SV_annotation.nf │ ├── SV_split_vcf_by_chr.nf │ ├── Vcftools_TsTv_by_qual.nf │ ├── count_bcftools_stats.nf │ ├── count_variants_gatk.nf │ ├── count_variants_gatk_2.nf │ ├── count_variants_vcftools.nf │ ├── gnomad_SV_frequency_table.nf │ ├── gvcf_txt.nf │ ├── index_vcf.nf │ ├── multiqc_pop.nf │ ├── plink_sex_inference.nf │ ├── sample_QC.R │ ├── sample_QC.nf │ ├── sample_QC_220504.R │ ├── samtools_fixmate.nf │ ├── split_tsv_by_chr.nf │ └── split_vcf_by_chr.nf ├── bcf_to_vcf.nf ├── bwa_index.nf ├── deepvariant.nf ├── expansion_hunter.nf ├── fastqc.nf ├── gnomad_frequency_table.nf ├── list_vcfs_txt.nf ├── melt.nf ├── merge_samples.nf ├── merge_samples_miss0.nf ├── mosdepth.nf ├── multiqc_indiv.nf ├── shift_back.R └── shift_back.nf ├── nextflow.config ├── nextflow.config_experimental ├── severity_table.tsv ├── singularity ├── README └── picard_r.def ├── subworkflow ├── Initialisation.nf ├── MT.nf ├── Mapping.nf ├── SNV.nf └── SV.nf ├── supplementary_information ├── GRCh37_specific_files.md ├── GRCh38_specific_files.md ├── Mitochondrial_references.md ├── Variant_catalogue_figure.png ├── Variant_catalogue_supp_figure.pdf └── software_information.md └── test_case ├── 20_samples_information ├── 80_samples_information ├── MT ├── MT_filtered_frequ_only_MT_annotation_table_merged_chrM.vcf └── MT_stats.txt ├── SNV ├── SNV_filtered_frequ_only_SNV_annotation_table_merged_22_truncated.vcf ├── SNV_indel_QC_report.txt ├── variant_QC_Allele number per variant - Unfiltered SNV.html ├── variant_QC_Call rate per variant - Unfiltered SNV.html ├── variant_QC_Expected frequency of heterozygous samples under Hardy-Weinberg equilibrium_Number of heterozygous samples per variant - Unfiltered SNV.html ├── variant_QC_Mean Depth per variant - Unfiltered SNV.html ├── variant_QC_Mean Genotype Quality per variant - Unfiltered SNV.html └── variant_QC_p-value from two-sided test of Hardy-Weinberg equilibrium per variant - Unfiltered SNV.html ├── SV ├── MEI │ ├── MEI_QC_Expected frequency of heterozygous samples under Hardy-Weinberg equilibrium_Number of heterozygous samples per variant.html │ ├── MEI_QC_Mean Depth per variant.html │ ├── MEI_QC_p-value from two-sided test of Hardy-Weinberg equilibrium per variant.html │ ├── MEI_QC_report.txt │ ├── MEI_filtered_frequ_only_MEI_annotation_table_merged_22.vcf │ └── MEI_filters_report.txt ├── STR │ └── STR_Version_0.0.1.vcf └── SV │ ├── SV_QC_Allele number per SV.html │ ├── SV_QC_Call rate per SV.html │ ├── SV_QC_Expected frequency of heterozygous samples under Hardy-Weinberg equilibrium_Number of heterozygous samples per SV.html │ ├── SV_QC_Mean Depth per SV.html │ ├── SV_QC_p-value from two-sided test of Hardy-Weinberg equilibrium per SV.html │ ├── SV_QC_report.txt │ ├── SV_filtered_frequ_only_SV_annotation_table_merged_22.vcf │ └── SV_filters.txt ├── cram_to_fastq.sh ├── flowchart.png ├── report.html ├── timeline.html └── trace.txt /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/wassermanlab/Variant_catalogue_pipeline/HEAD/.gitattributes -------------------------------------------------------------------------------- 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