├── .gitignore ├── README.md ├── abstracts ├── azure │ └── a4r_grant.org ├── bosc_2015_bcbio_prioritization │ ├── Makefile │ ├── chapman_bosc.md │ └── header.tex ├── bosc_2016_bcbio_cwl │ ├── Makefile │ ├── chapman_bosc.md │ ├── chapman_bosc.pdf │ └── header.tex ├── bosc_2017_bcbio_integration │ ├── Makefile │ ├── chapman_bosc.md │ ├── chapman_bosc.pdf │ └── header.tex ├── bosc_2018_bcbio_validation │ ├── Makefile │ ├── chapman_bosc.md │ ├── chapman_bosc.pdf │ └── header.tex ├── hackathon_workshop_2017 │ ├── Makefile │ ├── chapman_codefest.md │ ├── chapman_codefest.pdf │ └── header.tex └── hackathon_workshop_2018 │ ├── acmcopyright.sty │ ├── chapman_codefest.pdf │ ├── chapman_codefest.tex │ └── sigchi-ext.cls ├── align ├── Alignments.py ├── Phast.py ├── adaptor_trim.py └── maf_sort_by_size.py ├── biopython ├── CodingRegion.py ├── glimmer.gff ├── glimmer_to_proteins.py ├── glimmergff_to_proteins.py └── ref.fa ├── biosql ├── BioSQL-SQLAlchemy_definitions.py └── auth │ └── biosql_authorization.sql ├── biosql_ontologies ├── biosql_ontologies.txt ├── example_files │ ├── 18463287.rdf │ └── Q21307.rdf ├── feature_table │ ├── FT_SO_map.txt │ └── FT_index.html ├── genbank_ontology_map.txt ├── genbank_to_ontology.py ├── ontologies │ ├── dcterms.rdf │ ├── rdf-schema.rdf │ └── so.obo └── sparta.py ├── biostar ├── bed-hadoop │ ├── .gitignore │ ├── README.md │ ├── project.clj │ ├── src │ │ └── bed_hadoop │ │ │ └── core.clj │ └── test │ │ ├── one.bed │ │ └── two.bed ├── biostar.ngschallenge │ ├── .gitignore │ ├── README.md │ ├── config │ │ └── run_info.yaml │ ├── project.clj │ └── src │ │ └── biostar │ │ └── ngschallenge │ │ └── core.clj ├── fasta │ ├── fasta_counter.clj │ ├── fasta_counter_nolibs.clj │ └── fasta_splitter.clj └── findorf │ ├── .gitignore │ ├── README.md │ ├── project.clj │ ├── src │ └── findorf │ │ └── core.clj │ └── test │ └── test-in.fa ├── classify └── pubmed_related_group.py ├── cv ├── chapman_cv.pdf ├── chapman_cv.tex ├── chapman_research_statement.org └── chapman_research_statement.pdf ├── distblast ├── README.md ├── bcbio │ ├── __init__.py │ └── phylo │ │ ├── __init__.py │ │ └── blast.py ├── ec2 │ └── cluster_install_distblast.py ├── hadoop │ ├── distblast_pipes.py │ ├── distblast_streaming.py │ └── hadoop_run.py ├── scripts │ ├── blast_all_by_all.py │ ├── blast_cross_orgs.py │ ├── filter_by_transcript.py │ ├── homolog_seq_retrieval.py │ └── retrieve_org_dbs.py └── setup.py ├── galaxy ├── convert_library_dbkey.py └── galaxy_fabfile.py ├── gff ├── BCBio │ ├── GFF │ │ ├── GFFOutput.py │ │ ├── GFFParser.py │ │ ├── __init__.py │ │ └── _utils.py │ └── __init__.py ├── LICENSE ├── MANIFEST.in ├── README.rst ├── Scripts │ └── gff │ │ ├── access_gff_index.py │ │ ├── genbank_to_gff.py │ │ ├── gff2_to_gff3.py │ │ ├── gff_to_biosql.py │ │ └── gff_to_genbank.py ├── Tests │ ├── GFF │ │ ├── F3-unique-3.v2.gff │ │ ├── c_elegans_WS199_ann_gff.txt │ │ ├── c_elegans_WS199_dna_shortened.fa │ │ ├── c_elegans_WS199_shortened_gff.txt │ │ ├── ensembl_gtf.txt │ │ ├── glimmer_nokeyval.gff3 │ │ ├── hybrid1.gff3 │ │ ├── hybrid2.fa │ │ ├── hybrid2.gff3 │ │ ├── jgi_gff2.txt │ │ ├── mouse_extra_comma.gff3 │ │ ├── ncbi_gff3.txt │ │ ├── problem_sequence_region.gff3 │ │ ├── spaces.gff3 │ │ ├── trans_splicing.gff3 │ │ ├── transcripts.gff3 │ │ ├── unescaped-semicolon.gff3 │ │ ├── wormbase_gff2.txt │ │ └── wormbase_gff2_alt.txt │ └── test_GFFSeqIOFeatureAdder.py ├── distribute_setup.py └── setup.py ├── hg38alt ├── GRCh38p12.bed ├── GRCh38p12.tsv ├── README.md ├── annotate_with_alts.py ├── grc_to_bed.py └── hg38.fa.fai ├── keyval_testing ├── couchdb_get_freqs.py ├── freq_to_couchdb.py ├── freq_to_mongodb.py ├── freq_to_tyrant.py ├── mongodb_get_freqs.py └── tyrant_get_freqs.py ├── nextgen ├── README.md ├── bcbio │ ├── __init__.py │ ├── bam │ │ ├── __init__.py │ │ ├── counts.py │ │ ├── fastq.py │ │ └── trim.py │ ├── broad │ │ ├── __init__.py │ │ ├── metrics.py │ │ └── picardrun.py │ ├── distributed │ │ ├── __init__.py │ │ ├── ipython.py │ │ ├── ipythontasks.py │ │ ├── lsf.py │ │ ├── manage.py │ │ ├── messaging.py │ │ ├── multitasks.py │ │ ├── sge.py │ │ ├── split.py │ │ ├── tasks.py │ │ └── transaction.py │ ├── galaxy │ │ ├── __init__.py │ │ └── api.py │ ├── hmmer │ │ ├── __init__.py │ │ └── search.py │ ├── log │ │ └── __init__.py │ ├── ngsalign │ │ ├── __init__.py │ │ ├── bowtie.py │ │ ├── bowtie2.py │ │ ├── bwa.py │ │ ├── mosaik.py │ │ ├── novoalign.py │ │ ├── split.py │ │ └── tophat.py │ ├── picard │ │ ├── __init__.py │ │ ├── metrics.py │ │ └── utils.py │ ├── pipeline │ │ ├── __init__.py │ │ ├── alignment.py │ │ ├── config_utils.py │ │ ├── demultiplex.py │ │ ├── fastq.py │ │ ├── lane.py │ │ ├── main.py │ │ ├── merge.py │ │ ├── qcsummary.py │ │ ├── run_info.py │ │ ├── sample.py │ │ ├── shared.py │ │ ├── storage.py │ │ ├── toplevel.py │ │ └── variation.py │ ├── rnaseq │ │ ├── __init__.py │ │ └── cufflinks.py │ ├── solexa │ │ ├── __init__.py │ │ ├── flowcell.py │ │ └── samplesheet.py │ ├── structural │ │ ├── __init__.py │ │ └── hydra.py │ ├── utils.py │ └── variation │ │ ├── __init__.py │ │ ├── annotation.py │ │ ├── cortex.py │ │ ├── effects.py │ │ ├── ensemble.py │ │ ├── freebayes.py │ │ ├── genotype.py │ │ ├── multi.py │ │ ├── phasing.py │ │ ├── realign.py │ │ ├── recalibrate.py │ │ ├── samtools.py │ │ ├── split.py │ │ └── varscan.py ├── config │ ├── bcbio_sample.yaml │ ├── bcbio_system.yaml │ ├── examples │ │ └── NA12878-ensemble.yaml │ ├── transfer_info.yaml │ └── universe_wsgi.ini ├── docs │ ├── Makefile │ ├── conf.py │ ├── contents │ │ ├── configuration.rst │ │ ├── installation.rst │ │ ├── internals.rst │ │ ├── parallel.rst │ │ └── testing.rst │ └── index.rst ├── scripts │ ├── bam_to_wiggle.py │ ├── barcode_sort_trim.py │ ├── bcbio_nextgen.py │ ├── bcbio_nextgen_install.py │ ├── cg_svevents_to_vcf.py │ ├── hydra_to_vcf.py │ ├── illumina_finished_msg.py │ ├── monthly_billing_report.py │ ├── nextgen_analysis_server.py │ ├── plink_to_vcf.py │ ├── solexa_qseq_to_fastq.py │ ├── upload_to_galaxy.py │ └── utils │ │ ├── analyze_quality_recal.py │ │ ├── bam_to_fastq_region.py │ │ ├── broad_redo_analysis.py │ │ ├── build_compare_vcf.py │ │ ├── build_gatk_jar.sh │ │ ├── collect_metrics_to_csv.py │ │ ├── convert_samplesheet_config.py │ │ ├── rename_samples.py │ │ ├── resort_bam_karyotype.py │ │ ├── sort_gatk_intervals.py │ │ └── summarize_gemini_tstv.py └── tests │ ├── bed2interval │ ├── mouse.interval │ ├── test_bed2interval.py │ └── test_bed2interval.yaml │ ├── data │ ├── 110221_empty_FC12345AAXX │ │ ├── 1_110221_FC12345AAXX_fastq.txt │ │ ├── 2_110221_FC12345AAXX_fastq.txt │ │ └── 3_110221_FC12345AAXX_fastq.txt │ ├── automated │ │ ├── post_process-sample.yaml │ │ ├── run_info-bam.yaml │ │ ├── run_info-empty.yaml │ │ ├── run_info-rnaseq.yaml │ │ ├── run_info-variantcall.yaml │ │ ├── run_info.yaml │ │ ├── tool-data │ │ │ ├── bowtie_indices.loc │ │ │ ├── bwa_index.loc │ │ │ ├── mosaik_index.loc │ │ │ └── sam_fa_indices.loc │ │ ├── universe_wsgi.ini │ │ └── variant_regions-variantcall.bed │ ├── fastq │ │ └── illumina │ │ │ ├── test_fastq_1.fastq │ │ │ └── test_fastq_2.fastq │ ├── illumina_samplesheet.csv │ ├── illumina_samplesheet_fcid_mixed.csv │ ├── illumina_samplesheet_sampleref_mixed.csv │ ├── organisms │ │ └── mouse │ │ │ ├── mouse.bam │ │ │ ├── mouse.bed │ │ │ └── mouse.gtf │ ├── run_info-alternatives.yaml │ └── structural │ │ ├── NA12878-hydra.txt │ │ └── NA12878-hydra.vcf │ ├── split_vcf │ ├── data │ │ ├── NA12878-hydra.vcf │ │ ├── chr22_correct.vcf │ │ └── chrM_correct.vcf │ ├── test_split_vcf.py │ └── test_split_vcf.yaml │ ├── test_SequencingDump.py │ ├── test_automated_analysis.py │ ├── test_fastq.py │ ├── test_pipeline.py │ └── test_utils.py ├── papers └── bcbio-nextgen │ ├── Makefile │ ├── chapman_bcbio.bib │ ├── chapman_bcbio.pdf │ ├── chapman_bcbio.tex │ ├── fix_bibfile.py │ ├── frontiersSCNS.cls │ ├── frontiersinSCNS&ENG.bst │ ├── parallel-genome.png │ ├── validation-gatkprep.png │ └── validation-noprep.png ├── posters ├── beltrame_ESHG_poster_05_2014.reduced.pdf └── chi2018_hackathon │ ├── codefest_chi2018_hackathon.pdf │ └── codefest_chi2018_hackathon.svg ├── posts ├── aws_timings.org ├── callers_compare_2.org ├── callers_compare_3.org ├── calling_pipeline_compare │ ├── calling_pipeline_compare.org │ ├── grading-summary-prep-Indel.pdf │ ├── grading-summary-prep-SNP.pdf │ ├── grading-summary-prep-aligner-Indel.pdf │ ├── grading-summary-prep-aligner-SNP.pdf │ ├── grading-summary-prep-alignerdiff.png │ ├── grading-summary-prep-bamprep-Indel.pdf │ ├── grading-summary-prep-bamprep-SNP.pdf │ ├── grading-summary-prep-bamprepdiff.png │ ├── grading-summary-prep-caller-Indel.pdf │ ├── grading-summary-prep-caller-SNP.pdf │ ├── grading-summary-prep-callerdiff.png │ └── grading-summary-prep.csv ├── cancer_validation.org ├── conferences │ ├── aws-lifesciences2016.org │ ├── bioindocker_day1.org │ ├── bioindocker_day2.org │ ├── bosc2013_day1a.org │ ├── bosc2013_day1b.org │ ├── bosc2013_day2a.org │ ├── bosc2013_day2b.org │ ├── bosc2014_day1a.org │ ├── bosc2014_day1b.org │ ├── bosc2014_day2a.org │ ├── bosc2014_day2b.org │ ├── bosc2015_day1a.org │ ├── bosc2015_day1b.org │ ├── bosc2015_day2a.org │ ├── bosc2015_day2b.org │ ├── bosc2016_day1a.org │ ├── bosc2016_day1b.org │ ├── bosc2016_day2a.org │ ├── bosc2016_day2b.org │ ├── bosc2017_day1a.md │ ├── bosc2017_day1b.md │ ├── bosc2017_day2a.md │ ├── bosc2018_day1a.md │ ├── bosc2018_day2.md │ ├── bosc_codefest_report.org │ ├── chihackathon2018.md │ ├── dnanexus2017_day1.md │ ├── dnanexus2017_day2.md │ ├── gcc2014_day1.org │ ├── gcc2014_day1b.org │ ├── giab2013.org │ ├── mtsinai_workshop.org │ ├── nih_data_commons.md │ ├── nih_data_commons_notes.md │ ├── scipy2013_day1.org │ └── scipy2013_day2.org ├── hg38_validation.md ├── hg38_validation.org ├── joint_validation.org ├── reproducbility_docker.org ├── scaling_wgs_pipelines.org ├── seminars │ ├── big2018_2019.org │ ├── big_inma_proteomics2018.md │ ├── big_stuart_agbt2018.md │ ├── cancer_gatz.md │ ├── park_sv_cancer.md │ ├── shalek_singlecell.md │ ├── tumor_heterogeneity_carter.md │ └── variant_modeling.md └── sv_validation.org ├── qualbin ├── README.md ├── compare_discordants_to_replicates.py ├── plot_alignment_qualbin.R ├── plot_variant_qualbin.R └── qualbin_discordant_check.yaml ├── rest_apis ├── ensembl_remote_rest.py ├── find_geo_data.py └── uniprot_query_cluster.py ├── semantic ├── biomart.py ├── intermine.py ├── sadi_sparql.py ├── sparta_ex.py └── systemsbio.py ├── stats ├── count_diffexp.py ├── count_diffexp_general.py ├── diffexp_example-diffs.csv ├── diffexp_example-go_map.txt ├── diffexp_example-go_results.txt ├── diffexp_example.csv ├── diffexp_go_analysis.py └── install_packages.R ├── svplot ├── extract_svs.py └── plot_sv_circos.R ├── talks ├── 2015_iowast_career │ ├── chapman_career.org │ ├── chapman_career.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ └── images7 │ │ ├── Austrian_pine.jpg │ │ ├── Genegun.jpg │ │ ├── arvados_overview.png │ │ ├── bcbio_commits.png │ │ ├── bcbio_issues.png │ │ ├── build38_reddit.png │ │ ├── build38_release.png │ │ ├── cancer_multiple.png │ │ ├── careers.jpg │ │ ├── dream_challenge.png │ │ ├── dream_syn4.png │ │ ├── exac.png │ │ ├── ga4gh.png │ │ ├── galaxy_cwl.png │ │ ├── harvard_chan.png │ │ ├── hg38_collapsed_repeats.jpg │ │ ├── hg38_collapsed_repeats.png │ │ ├── hg38_val.png │ │ ├── hg38_val_giab.png │ │ ├── hla_naming.png │ │ ├── rare_disease.png │ │ ├── sv_dream_del.png │ │ ├── sv_dream_ins.png │ │ ├── sv_dream_old.png │ │ ├── sv_giab_del.png │ │ ├── sv_val.png │ │ ├── vardict_filter_dp.png │ │ ├── vardict_filter_nmmq.png │ │ ├── vardict_filter_nmmq.svg │ │ ├── vardict_filter_nmmq_fp.png │ │ ├── vardict_filter_nmmq_tp.png │ │ ├── vardict_filter_qual.png │ │ ├── vardict_val.png │ │ └── vardict_val_orig.png ├── abcd2014_bcbio_nextgen │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ ├── images │ └── images2 │ │ ├── docker-parallel.png │ │ ├── gatk_changes.png │ │ ├── gatk_changes.svg │ │ ├── install_issues.png │ │ └── install_want.png ├── arvados2013_bcbio_nextgen │ ├── chapman_arvadossum_bcbio.org │ ├── chapman_arvadossum_bcbio.pdf │ └── images │ │ ├── bcbio_nextgen_highlevel.png │ │ ├── community.png │ │ ├── dtc_genomics.jpg │ │ ├── gatk_changes.png │ │ ├── gcat_comparison.png │ │ ├── gemini.png │ │ ├── huge_seq.png │ │ ├── minprep-callerdiff.png │ │ ├── parallel-clustertypes.png │ │ └── schedulers.png ├── az2016_medi │ ├── az2016_medi.org │ ├── az2016_medi.pdf │ ├── images │ ├── images7 │ └── images8 ├── bcbb2015_bcbio │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ └── images7 ├── bcbio2019_recomendations │ ├── bcbio2019_recommendations.org │ ├── bcbio2019_recommendations.pdf │ └── images │ │ ├── germline-validation.png │ │ ├── purecn-loh.png │ │ └── vardict-octopus-tumoronly.png ├── big2014_bcbio_val │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ └── images7 │ │ ├── 20150204_HBC_Team.png │ │ ├── bcbio_contributors.png │ │ ├── benchmark_cpu_plot.png │ │ ├── benchmark_io_plot.png │ │ ├── cancer-svs.png │ │ ├── cancer_validate.png │ │ ├── chanjo.png │ │ ├── dream_challenge.png │ │ ├── exvcf.png │ │ ├── freebayes_improve-syn3-tumor.png │ │ ├── freebayes_lodfreqfilter-syn3-tumor.png │ │ ├── ga4gh.png │ │ ├── gemini_overview.png │ │ ├── joint.png │ │ ├── method_compare-gatk-NA12878.png │ │ ├── mutect_contrib.png │ │ ├── squaredoff.png │ │ └── svval.png ├── big2015_bcbio │ ├── big2015_bcbio.org │ ├── big2015_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ └── images9 ├── big2016_bcbio_cwl │ ├── big2016_bcbiocwl.org │ ├── big2016_bcbiocwl.pdf │ ├── images │ ├── images10 │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ └── images9 ├── big2017_bcbio_cwl │ ├── big2017_bcbio_cwl.org │ ├── big2017_bcbio_cwl.pdf │ ├── images │ ├── images10 │ ├── images11 │ ├── images12 │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ └── images9 ├── biogen2014_bcbio_nextgen │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ ├── images │ ├── images2 │ └── images3 │ │ ├── bcbio_nextgen_highlevel.png │ │ ├── bcbio_nextgen_highlevel.svg │ │ ├── fas_odyssey.png │ │ ├── rnaseq_config.png │ │ └── variantcall_config.png ├── bioindocker2015_bcbio │ ├── chapman_bioindocker.org │ ├── chapman_bioindocker.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ └── images7 ├── bosc2013_bcbio_nextgen │ ├── build.py │ ├── chapmanb_bosc2013_bcbio.html │ ├── chapmanb_bosc2013_bcbio.ipynb │ ├── chapmanb_bosc2013_bcbio.org │ └── images │ │ ├── 4.1_stormseq.png │ │ ├── bcbio_nextgen_highlevel.png │ │ ├── bcbio_nextgen_highlevel.svg │ │ ├── community.png │ │ ├── dtc_genomics.jpg │ │ ├── galaxy_pipeline.png │ │ ├── gatk_changes.png │ │ ├── gatk_changes.svg │ │ ├── gcat_comparison.png │ │ ├── gemini.png │ │ ├── grading-summary-prep-callerdiff.png │ │ ├── huge_seq.png │ │ ├── o8.png │ │ ├── parallel-clustertypes.png │ │ ├── parallel-genome.png │ │ ├── schedulers.png │ │ └── schedulers.svg ├── bosc2014_bcbio │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ └── images4 │ │ └── install_issues.png ├── bosc2015_bcbio_prioritize │ ├── bosc2015_bcbio_prioritize.org │ ├── bosc2015_bcbio_prioritize.pdf │ └── images │ │ ├── CWL-Logo-4k.png │ │ ├── arvados-overview.png │ │ ├── bcbio-cwl.png │ │ ├── bcbio-cwl.svg │ │ ├── bcbio_commits_mar2016.png │ │ ├── bcbio_commits_sep2016.png │ │ ├── bcbio_github_mar2016.png │ │ ├── bcbio_github_sep2016.png │ │ ├── bcbio_issues_mar2016.png │ │ ├── bcbio_issues_sep2016.png │ │ ├── bcbio_nextgen_highlevel.png │ │ ├── bcbio_pipelines.png │ │ ├── biology-of-cancer.jpg │ │ ├── gemini_overview.png │ │ ├── hla-vg-graph.png │ │ ├── nature14169-sf2.jpg │ │ ├── prioritize-overview.png │ │ ├── prioritize-overview.svg │ │ ├── sv-dup-val.png │ │ └── vg-variant-calls.png ├── bosc2016_bcbio_cwl │ ├── chapman_bosc2106_bcbio.org │ ├── chapman_bosc2106_bcbio.pdf │ └── images │ │ ├── Network_Community_Structure.png │ │ ├── WDL-scatter.jpg │ │ ├── WDL-workflow.png │ │ ├── abstractions.png │ │ ├── abstractions.svg │ │ ├── arvados.png │ │ ├── bcbio.png │ │ ├── biostars-galaxy.png │ │ ├── biostars.png │ │ ├── bosc2016.png │ │ ├── cbioportal_logo.png │ │ ├── cwl_pipeline_example.png │ │ ├── fitness.png │ │ ├── gatk-giab-NA12878.png │ │ ├── gatk-giab-NA24385.png │ │ ├── gnomad.png │ │ ├── grading-example.png │ │ ├── grading-example.svg │ │ ├── grading-summary-24385.png │ │ ├── grading-summary-example.png │ │ ├── nextflow_cwl.png │ │ ├── synapse.png │ │ └── usegalaxy.png ├── bosc2017_bcbio_interoperate │ ├── Codefest_2107_report.pdf │ ├── chapmanb_bcbio_interoperate.org │ ├── chapmanb_bcbio_interoperate.pdf │ ├── images10 │ ├── images12 │ │ ├── CW-dream-banner.jpg │ │ ├── analysis_to_data.png │ │ ├── analysis_to_data.svg │ │ ├── apoe.png │ │ ├── arvados.png │ │ ├── arvados_pgp.png │ │ ├── bcbio_commits_oct2018.png │ │ ├── bcbio_contrib_apr2018.png │ │ ├── bcbio_inprogress.png │ │ ├── bcbio_inprogress.svg │ │ ├── bcbio_issues_apr2018.png │ │ ├── bcbio_issues_oct2018.png │ │ ├── bcbio_supported.png │ │ ├── bcbio_supported.svg │ │ ├── chr19_klk15.png │ │ ├── cromwell-cwl.png │ │ ├── cromwell.png │ │ ├── cwltool.png │ │ ├── deepvariant.png │ │ ├── dnanexus-medium.png │ │ ├── dnanexus-parallel-full.png │ │ ├── dnanexus-parallel-longtail-fixed.png │ │ ├── dnanexus-parallel-longtail.png │ │ ├── dnanexus-parallel-region.png │ │ ├── dnanexus-parallel-subworkflow.png │ │ ├── dnanexus_monitor.png │ │ ├── existing_workflows.png │ │ ├── existing_workflows2.png │ │ ├── galaxy.png │ │ ├── galaxy_overview.png │ │ ├── gatk_cnn.png │ │ ├── gccbosc2018.png │ │ ├── giab-joint-recal.csv │ │ ├── giab-joint-recal.png │ │ ├── grading-summary-gm1.png │ │ ├── huD57BBF-KLK15-DEL-plaudit.png │ │ ├── hud57bbf-klk15-del.png │ │ ├── klk15_expression.png │ │ ├── klk15_wikipedia.png │ │ ├── nextflow.png │ │ ├── nextflow_overview.png │ │ ├── open-bio.png │ │ ├── openhumans.png │ │ ├── pgp.png │ │ ├── pgp_huD57BBF.png │ │ ├── pgp_huD57BBF_conditions.png │ │ ├── rabix-deprecation.png │ │ ├── rabix.png │ │ ├── snakemake_overview.png │ │ ├── toil.png │ │ ├── vardict-filter-validation.png │ │ └── wdl-logo_white.png │ ├── images3 │ └── images9 ├── bosc2018_bcbio_training │ ├── bosc2018_bcbio_training.org │ ├── bosc2018_bcbio_training.pdf │ ├── images │ ├── images10 │ ├── images11 │ ├── images12 │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ └── images9 ├── bosc2018_bcbio_validate │ ├── chapman_bcbio_validate.org │ ├── chapman_bcbio_validate.pdf │ └── images │ │ ├── bcbio_validation_plot-dv.py │ │ ├── bcbio_validation_plot-gatk4.py │ │ ├── bcbio_validation_plot-ras.py │ │ ├── cwl-variant.png │ │ ├── grading-summary-dv.csv │ │ ├── grading-summary-dv.png │ │ ├── grading-summary-gj1.csv │ │ ├── grading-summary-gj1.png │ │ ├── grading-summary-ras.csv │ │ └── grading-summary-ras.png ├── broad_engineering2016_bcbio │ ├── broad2016_bcbio.org │ ├── broad2016_bcbio.pdf │ ├── images │ ├── images10 │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ └── images9 ├── cdnm2016_bcbio │ ├── cdnm2016_bcbio.org │ ├── cdnm2016_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ └── images9 ├── cgc2017_bcbio_cwl │ ├── cgc2017_bcbiocwl.org │ ├── cgc2017_bcbiocwl.pdf │ ├── images │ ├── images10 │ ├── images11 │ │ ├── bcbio_commits_apr2017.png │ │ ├── bcbio_issues_apr2017.png │ │ ├── bosc2017.png │ │ ├── cgc.png │ │ ├── cgc_biodata.png │ │ ├── cgc_project.png │ │ ├── efficiency.png │ │ ├── gatk_bp.png │ │ └── nextflow_comparison.png │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ └── images9 ├── codefest2013_report │ ├── codefest2013_report.html │ └── codefest2013_report.org ├── cshl2015_bcbio │ ├── cshl2015_bcbio.org │ ├── cshl2015_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ └── images9 ├── curoverse2016bb_bcbio │ ├── curoverse2016bb_bcbio.org │ ├── curoverse2016bb_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ └── images9 ├── debianmed2014_cloudbiolinux │ ├── chapman_cbl.org │ ├── chapman_cbl.pdf │ └── images │ │ └── Dogfooding-Aug-2013.png ├── dfci2018_bcbio │ ├── dfci2018_bcbio_chapman.org │ ├── dfci2018_bcbio_chapman.pdf │ ├── images12 │ └── images3 ├── gcc2014_bcbio │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ ├── images │ ├── images2 │ │ ├── bcbio_tool.png │ │ └── parallel-genome.png │ └── images3 ├── gcc2014_cloudbiolinux │ ├── chapman_cbl.org │ ├── chapman_cbl.pdf │ └── images │ │ ├── cbl.png │ │ ├── flavor-brew.png │ │ ├── flavor-demo.png │ │ ├── flavor-fabricrc.png │ │ ├── flavor-main.png │ │ ├── flavor.png │ │ ├── homebrew-cbl.png │ │ ├── homebrew-science.png │ │ ├── homepage-docker-logo.png │ │ ├── linuxbrew.png │ │ ├── recipe-vep.png │ │ ├── recipe-vt.png │ │ ├── yaml-config-dir.png │ │ └── yaml-config-ex.png ├── ginkgo_dataorg │ ├── ginkgo_dataorg.org │ ├── ginkgo_dataorg.pdf │ └── images │ │ ├── ag_energy.png │ │ ├── animal_impact.png │ │ ├── assay_hodur.png │ │ ├── assay_model.png │ │ ├── assay_notebook.png │ │ ├── assay_output.png │ │ ├── assay_workflow.png │ │ ├── bao_od600.png │ │ ├── bwa_cwl.png │ │ ├── bwa_shell.png │ │ ├── data_cleaning.png │ │ ├── data_work.png │ │ ├── dataanalysis_thread.png │ │ ├── dataanalysis_units.jpg │ │ ├── datomic.png │ │ ├── ginkgobioworks.png │ │ ├── ilovegmos.png │ │ ├── ipcc.png │ │ ├── joynbio.png │ │ ├── json_xml.png │ │ ├── jupyter_ml.png │ │ ├── mco_od600.png │ │ ├── motif.png │ │ ├── nitrogen_runoff.png │ │ └── scigraph.png ├── gsg2015_bcbio_nextgen │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ └── images7 ├── heterogeneity2017 │ ├── heterogeneity2017_bcbio.org │ ├── heterogeneity2017_bcbio.pdf │ └── images │ │ ├── aml31_depth.jpg │ │ ├── ascat_sunrise.png │ │ ├── log2_baf_plot.jpg │ │ └── phylowgs_het_overview.png ├── intel2014_bcbio │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ └── images5 │ │ ├── SNV_calling.png │ │ ├── bcbio_github.png │ │ ├── clear_box.JPG │ │ ├── clear_box.jpg │ │ ├── exome_proportion.png │ │ ├── human_genome.png │ │ ├── infiniband.jpg │ │ ├── ipython_zmq.png │ │ ├── reads.png │ │ └── workflowprofiler.png ├── mtsinai2013_bcbio_nextgen │ ├── chapman_mtsinai_bcbio.org │ ├── chapman_mtsinai_bcbio.pdf │ ├── images │ │ ├── aws.png │ │ ├── bcbio_align_parallel.png │ │ ├── bcbio_align_parallel.svg │ │ ├── bcbio_nextgen_highlevel.png │ │ ├── bcbio_parallel_overview.png │ │ ├── bcbio_parallel_overview.svg │ │ ├── community-contribute.png │ │ ├── community-docs.png │ │ ├── community.png │ │ ├── dell-ai-hpc.png │ │ ├── dtc_genomics.jpg │ │ ├── gatk_changes.png │ │ ├── gcat_comparison.png │ │ ├── gemini.png │ │ ├── homepage-docker-logo.png │ │ ├── huge_seq.png │ │ ├── minprep-callerdiff.png │ │ ├── parallel-genome.png │ │ └── schedulers.png │ └── mtsinai_workshop_flyer.pdf ├── ngscourse2015_teaching │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ │ ├── GRCh37.jpg │ │ ├── GRCh38-advantages.jpg │ │ ├── GRCh38.jpg │ │ ├── MHC.png │ │ ├── Treatment_bottleneck.pdf │ │ ├── Utah-Pedigree-1463-with-NA12878.png │ │ ├── bwa-alts.png │ │ ├── cancer-somatic.png │ │ ├── discovar-graphs.jpg │ │ ├── freebayes.png │ │ ├── gatk-bp.png │ │ ├── gatk-hc.png │ │ ├── gatk-joint.png │ │ ├── gatk-license.png │ │ ├── gatk-reassembly.png │ │ ├── gatk-vqsr.png │ │ ├── gatk.png │ │ ├── gatk4-license.png │ │ ├── gatk4_na12878_hg38_validation.png │ │ ├── gatk_changes_gatk4.png │ │ ├── gatk_changes_gatk4.svg │ │ ├── hard-filters.png │ │ ├── mutations.png │ │ ├── svs.jpg │ │ ├── vcf-overview.png │ │ ├── vcf-representation.png │ │ ├── vep-consequences.jpg │ │ └── vg-graphs.png │ ├── variant_ngscourse.org │ └── variant_ngscourse.pdf ├── ngscourse2016_teaching │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ ├── images9 │ ├── ngscourse2016_teaching.org │ └── ngscourse2016_teaching.pdf ├── ngscourse2016b_teaching │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ ├── images9 │ ├── ngscourse2016b_teaching.org │ └── ngscourse2016b_teaching.pdf ├── ngscourse2017_teaching │ ├── images │ ├── images10 │ ├── images11 │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ ├── images9 │ ├── ngscourse2017_teaching.org │ └── ngscourse2017_teaching.pdf ├── ngscourse2018_teaching │ ├── images │ ├── images10 │ ├── images11 │ ├── images12 │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ ├── images9 │ ├── ngscourse2018_teaching.org │ └── ngscourse2018_teaching.pdf ├── novartis2014_bcbio_nextgen │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ └── images │ │ ├── arvados.png │ │ ├── aws.png │ │ ├── bcbio_align_parallel.png │ │ ├── bcbio_align_parallel.svg │ │ ├── bcbio_nextgen_highlevel.png │ │ ├── bcbio_nextgen_highlevel.svg │ │ ├── bcbio_parallel_overview.png │ │ ├── bcbio_parallel_overview.svg │ │ ├── community-contribute.png │ │ ├── community-docs.png │ │ ├── community.png │ │ ├── coverage_summary.png │ │ ├── dell-ai-hpc.png │ │ ├── dtc_genomics.jpg │ │ ├── galaxy.png │ │ ├── gatk_changes.png │ │ ├── gcat_comparison.png │ │ ├── gemini.png │ │ ├── giab.png │ │ ├── homepage-docker-logo.png │ │ ├── huge_seq.png │ │ ├── minprep-callerdiff.png │ │ ├── o8.png │ │ ├── parallel-genome.png │ │ └── schedulers.png ├── park2018_bcbio │ ├── images │ ├── images10 │ ├── images11 │ ├── images12 │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ ├── images9 │ ├── park2018_bcbio.org │ └── park2018_bcbio.pdf ├── pgp_analysis │ ├── images │ ├── images10 │ ├── images11 │ ├── images12 │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ ├── images7 │ ├── images8 │ ├── images9 │ ├── pgp_analysis.org │ └── pgp_analysis.pdf ├── pgsg2015_bcbio │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ ├── images6 │ └── images7 ├── reveal.js │ ├── css │ │ ├── print │ │ │ ├── paper.css │ │ │ └── pdf.css │ │ ├── reveal.css │ │ ├── reveal.min.css │ │ └── theme │ │ │ ├── beige.css │ │ │ ├── default.css │ │ │ ├── moon.css │ │ │ ├── night.css │ │ │ ├── serif.css │ │ │ ├── simple.css │ │ │ ├── sky.css │ │ │ ├── solarized.css │ │ │ ├── source │ │ │ ├── beige.scss │ │ │ ├── default.scss │ │ │ ├── moon.scss │ │ │ ├── night.scss │ │ │ ├── serif.scss │ │ │ ├── simple.scss │ │ │ ├── sky.scss │ │ │ └── solarized.scss │ │ │ └── template │ │ │ ├── mixins.scss │ │ │ ├── settings.scss │ │ │ └── theme.scss │ ├── js │ │ ├── reveal.js │ │ └── reveal.min.js │ ├── lib │ │ ├── css │ │ │ └── zenburn.css │ │ ├── font │ │ │ ├── league_gothic-webfont.eot │ │ │ ├── league_gothic-webfont.svg │ │ │ ├── league_gothic-webfont.ttf │ │ │ ├── league_gothic-webfont.woff │ │ │ └── league_gothic_license │ │ └── js │ │ │ ├── classList.js │ │ │ ├── head.min.js │ │ │ └── html5shiv.js │ └── plugin │ │ ├── highlight │ │ └── highlight.js │ │ ├── markdown │ │ ├── example.html │ │ ├── example.md │ │ ├── markdown.js │ │ └── marked.js │ │ ├── notes │ │ ├── notes.html │ │ └── notes.js │ │ ├── print-pdf │ │ └── print-pdf.js │ │ └── zoom-js │ │ └── zoom.js ├── scipy2013_bcbio_nextgen │ ├── scipy2013_bcbio_nextgen.html │ ├── scipy2013_bcbio_nextgen.org │ └── scipy2013_bcbio_nextgen.pdf └── uga2014_bcbio_open │ ├── chapman_bcbio.org │ ├── chapman_bcbio.pdf │ ├── images │ ├── images2 │ ├── images3 │ ├── images4 │ ├── images5 │ └── images6 │ ├── biodata_skills.jpg │ ├── bitbucket-logo.png │ ├── codon_devices.png │ ├── galaxy.png │ ├── github.png │ ├── hsph_logo_small.png │ ├── ipython.png │ ├── mozilla-science-lab.png │ ├── obf.jpg │ ├── rstudio.png │ ├── software-carpentry.png │ └── uga_paper.png ├── validation ├── NA12878-NGv3.yaml ├── README.md ├── plot_alignerparam_comparisons.r ├── plot_depth_ratio.py ├── plot_validation.py ├── plot_validation_results.r ├── prep_multicmp_results.py ├── prep_rm_subset.py ├── pull_bwa_novoalign_diffs.py ├── pull_bwa_novoalign_diffs.yaml ├── pull_shared_discordants.py ├── pull_shared_discordants.yaml └── sv │ ├── explore_wham.py │ └── sv_low_mappability.sh └── visualize └── blast_conservation_plot.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | nextgen/bcbio_nextgen.egg-info/ 3 | nextgen/build/ 4 | nextgen/dist/ 5 | nextgen/tests/data/100326* 6 | nextgen/tests/data/110106* 7 | nextgen/tests/data/110221* 8 | nextgen/tests/data/110907* 9 | nextgen/tests/data/genomes* 10 | nextgen/tests/test_automated_output/ 11 | distblast/*.egg-info/ 12 | distblast/build/ 13 | distblast/dist/ 14 | gff/*.egg-info/ 15 | gff/build/ 16 | gff/dist/ 17 | talks/*/*.tex 18 | .ipynb_checkpoints 19 | .ropeproject -------------------------------------------------------------------------------- /abstracts/bosc_2015_bcbio_prioritization/Makefile: -------------------------------------------------------------------------------- 1 | NAME=chapman 2 | build: 3 | pandoc ${NAME}_bosc.md -H header.tex -o ${NAME}_bosc.pdf 4 | 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-------------------------------------------------------------------------------- /biostar/bed-hadoop/test/one.bed: -------------------------------------------------------------------------------- 1 | chr1 20 30 2 | chr1 40 50 3 | chr2 30 40 4 | chr2 40 50 -------------------------------------------------------------------------------- /biostar/bed-hadoop/test/two.bed: -------------------------------------------------------------------------------- 1 | chr1 15 35 2 | chr2 45 55 -------------------------------------------------------------------------------- /biostar/biostar.ngschallenge/.gitignore: -------------------------------------------------------------------------------- 1 | /pom.xml 2 | *jar 3 | /lib 4 | /classes 5 | /native 6 | /.lein-failures 7 | /checkouts 8 | /.lein-deps-sum 9 | -------------------------------------------------------------------------------- /biostar/biostar.ngschallenge/README.md: -------------------------------------------------------------------------------- 1 | # biostar.ngschallenge 2 | 3 | Work for NGS challenge on BioStar: 4 | 5 | http://biostar.stackexchange.com/questions/15581/ngs-challenge-can-you-give-an-insight-about-this-imaginary-genetic-disease 6 | 7 | ## Usage 8 | 9 | $ lein deps 10 | $ lein run :find data/father_111217_biostar-variants.vcf 11 | data/mother_111217_biostar-variants.vcf 12 | data/child_111217_biostar-variants.vcf 13 | -------------------------------------------------------------------------------- /biostar/biostar.ngschallenge/config/run_info.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | fc_date: 111217 3 | fc_name: biostar 4 | details: 5 | - files: [child_1-ready.fq, child_2-ready.fq] 6 | description: child 7 | analysis: SNP calling 8 | genome_build: hg19 9 | algorithm: 10 | quality_format: Standard 11 | - files: [father_1-ready.fq, father_2-ready.fq] 12 | description: father 13 | analysis: SNP calling 14 | genome_build: hg19 15 | algorithm: 16 | quality_format: Standard 17 | - files: [mother_1-ready.fq, mother_2-ready.fq] 18 | description: mother 19 | analysis: SNP calling 20 | genome_build: hg19 21 | algorithm: 22 | quality_format: Standard 23 | -------------------------------------------------------------------------------- /biostar/biostar.ngschallenge/project.clj: -------------------------------------------------------------------------------- 1 | (defproject biostar.ngschallenge "0.0.1-SNAPSHOT" 2 | :description "Custom code for BioStar NGS challenge" 3 | :dependencies [[org.clojure/clojure "1.3.0"] 4 | [bcbio.variation "0.0.1-SNAPSHOT"]] 5 | :run-aliases {:find biostar.ngschallenge.core}) 6 | -------------------------------------------------------------------------------- /biostar/findorf/.gitignore: -------------------------------------------------------------------------------- 1 | pom.xml 2 | *jar 3 | lib 4 | classes 5 | -------------------------------------------------------------------------------- /biostar/findorf/project.clj: -------------------------------------------------------------------------------- 1 | (defproject findorf "0.0.1-SNAPSHOT" 2 | :description "ORF finder for BioStar question 5902" 3 | :dependencies [[org.clojure/clojure "1.2.0"] 4 | [org.clojure/clojure-contrib "1.2.0"] 5 | [org.biojava/biojava3-core "3.0.1"]] 6 | :repositories {"biojava" "http://www.biojava.org/download/maven/"} 7 | :run-aliases {:findorf findorf.core}) 8 | -------------------------------------------------------------------------------- /biostar/findorf/test/test-in.fa: -------------------------------------------------------------------------------- 1 | >t-1 2 | TTATACGTACGGTAA 3 | >t-2 4 | TTATAAGTACGGTAAG 5 | >t-3 6 | TTATAAGTAAGGTAAGC 7 | >t-r1 8 | TTATAAGTAAGTAAA 9 | >t-r2 10 | TGAGTTATAATTAAGTAAA 11 | >t-r3 12 | GTGATTAATTAAGTAAA 13 | >t-1-inner 14 | TAAATGATTAATCAATTATAA 15 | >EX720612.1 16 | ACATATAAGACGCACCAAATACTTTCTCCCTTCCCACCGCCGTCCACGTTCTCTCACATTATACAAGCAT 17 | CAACTTCAAACACATTGACAGAAAATGACATTATCAAATTCATCATATTACAAAGTTCTTGCATCCTTGA 18 | AGGTGGTAGCTCTTGCGGAAATGCTACTAACAGATCACACCGCCATTTTTCACATGCGTTCGGGATCTTC 19 | TTCCTCCTCTTCATACTCTTCATCATCGGCAGTTGCATCCTGGT 20 | -------------------------------------------------------------------------------- /cv/chapman_cv.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chapmanb/bcbb/320353c64ee0dc938113ca36f19b2e6de6b597be/cv/chapman_cv.pdf -------------------------------------------------------------------------------- /cv/chapman_research_statement.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chapmanb/bcbb/320353c64ee0dc938113ca36f19b2e6de6b597be/cv/chapman_research_statement.pdf -------------------------------------------------------------------------------- /distblast/bcbio/__init__.py: -------------------------------------------------------------------------------- 1 | """Blue collar bioinformatics main module. 2 | """ 3 | __import__('pkg_resources').declare_namespace(__name__) 4 | -------------------------------------------------------------------------------- /distblast/bcbio/phylo/__init__.py: -------------------------------------------------------------------------------- 1 | """General phylogenetic analysis code. 2 | """ 3 | -------------------------------------------------------------------------------- /distblast/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | """Setup script for distributed phylogenetic analysis by BLAST. 3 | """ 4 | from setuptools import setup, find_packages 5 | 6 | setup(name = "bcbio-phyloblast", 7 | version = "0.1.2", 8 | author = "Brad Chapman", 9 | author_email = "chapmanb@50mail.com", 10 | description = "Distributed BLAST for gene phylogeny estimation", 11 | license = "MIT", 12 | url = "http://bcbio.wordpress.com", 13 | namespace_packages = ["bcbio"], 14 | packages = find_packages(), 15 | scripts = ["scripts/blast_cross_orgs.py", 16 | "scripts/retrieve_org_dbs.py"], 17 | install_requires=[ 18 | "biopython >= 1.62", 19 | "PyYAML >= 3.10"] 20 | ) 21 | -------------------------------------------------------------------------------- /gff/BCBio/GFF/__init__.py: -------------------------------------------------------------------------------- 1 | """Top level of GFF parsing providing shortcuts for useful classes. 2 | """ 3 | from BCBio.GFF.GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple 4 | from BCBio.GFF.GFFOutput import GFF3Writer, write 5 | 6 | __version__ = "0.7.1" 7 | -------------------------------------------------------------------------------- /gff/BCBio/__init__.py: -------------------------------------------------------------------------------- 1 | """BCBio module 2 | """ 3 | -------------------------------------------------------------------------------- /gff/MANIFEST.in: -------------------------------------------------------------------------------- 1 | recursive-include BCBio *.py 2 | include distribute_setup.py 3 | include *.rst 4 | include LICENSE 5 | -------------------------------------------------------------------------------- /gff/Scripts/gff/genbank_to_gff.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | """Convert a GenBank file into GFF format. 3 | 4 | Usage: 5 | genbank_to_gff.py 6 | """ 7 | import sys 8 | import os 9 | 10 | from Bio import SeqIO 11 | from Bio import Seq 12 | 13 | from BCBio import GFF 14 | 15 | def main(gb_file): 16 | out_file = "%s.gff" % os.path.splitext(gb_file)[0] 17 | with open(out_file, "w") as out_handle: 18 | GFF.write(SeqIO.parse(gb_file, "genbank"), out_handle) 19 | 20 | if __name__ == "__main__": 21 | main(*sys.argv[1:]) 22 | -------------------------------------------------------------------------------- /gff/Tests/GFF/c_elegans_WS199_ann_gff.txt: -------------------------------------------------------------------------------- 1 | # modified GFF file to remove location coordinates and test annotations 2 | I Expr_profile experimental_result_region . . . + . expr_profile=B0019.1 3 | -------------------------------------------------------------------------------- /gff/Tests/GFF/glimmer_nokeyval.gff3: -------------------------------------------------------------------------------- 1 | ##gff-version 3 2 | ##sequence-region scaffold4215_3 1 6526 3 | scaffold4215_3 glimmer gene 3 62 . - . ID=GL0000006;Name=GL0000006;Lack 3'-end; 4 | scaffold4215_3 glimmer mRNA 3 62 . - . ID=GL0000006;Name=GL0000006;Parent=GL0000006;Lack 3'-end; 5 | scaffold4215_3 glimmer CDS 3 62 2.84 - 0 Parent=GL0000006;Lack 3'-end; 6 | scaffold4215_3 glimmer gene 124 1983 . - . ID=GL0000007;Name=GL0000007;Complete; 7 | -------------------------------------------------------------------------------- /gff/Tests/GFF/hybrid1.gff3: -------------------------------------------------------------------------------- 1 | ##gff-version 3 2 | ##sequence-region foo 1 100 3 | ##feature-ontology bar 4 | ##attribute-ontology baz 5 | ##source-ontology boo 6 | ##sequence-region chr17 62467934 62469545 7 | chr17 UCSC mRNA 62467934 62469545 . - . ID=A00469;Dbxref=AFFX-U133:205840_x_at,Locuslink:2688,Genbank-mRNA:A00469,Swissprot:P01241,PFAM:PF00103,AFFX-U95:1332_f_at,Swissprot:SOMA_HUMAN;Note=growth%20hormone%201;Alias=GH1 8 | chr17 UCSC CDS 62468039 62468236 . - 1 Parent=A00469 9 | chr17 UCSC CDS 62468490 62468654 . - 2 Parent=A00469 10 | chr17 UCSC CDS 62468747 62468866 . - 1 Parent=A00469 11 | chr17 UCSC CDS 62469076 62469236 . - 1 Parent=A00469 12 | chr17 UCSC CDS 62469497 62469506 . - 0 Parent=A00469 13 | ### 14 | ##FASTA 15 | >chr17 16 | GATTACA 17 | GATTACA 18 | -------------------------------------------------------------------------------- /gff/Tests/GFF/hybrid2.fa: -------------------------------------------------------------------------------- 1 | >lcl|chr17 2 | GATTACA 3 | GATTACA 4 | -------------------------------------------------------------------------------- /gff/Tests/GFF/hybrid2.gff3: -------------------------------------------------------------------------------- 1 | ##gff-version 3 2 | ##sequence-region foo 1 100 3 | ##feature-ontology bar 4 | ##attribute-ontology baz 5 | ##source-ontology boo 6 | ##sequence-region chr17 62467934 62469545 7 | chr17 UCSC mRNA 62467934 62469545 . - . ID=A00469;Dbxref=AFFX-U133:205840_x_at,Locuslink:2688,Genbank-mRNA:A00469,Swissprot:P01241,PFAM:PF00103,AFFX-U95:1332_f_at,Swissprot:SOMA_HUMAN;Note=growth%20hormone%201;Alias=GH1 8 | chr17 UCSC CDS 62468039 62468236 . - 1 Parent=A00469 9 | chr17 UCSC CDS 62468490 62468654 . - 2 Parent=A00469 10 | chr17 UCSC CDS 62468747 62468866 . - 1 Parent=A00469 11 | chr17 UCSC CDS 62469076 62469236 . - 1 Parent=A00469 12 | chr17 UCSC CDS 62469497 62469506 . - 0 Parent=A00469 13 | ### 14 | ##FASTA 15 | >lcl|chr17 16 | GATTACA 17 | GATTACA 18 | -------------------------------------------------------------------------------- /gff/Tests/GFF/jgi_gff2.txt: -------------------------------------------------------------------------------- 1 | chr_1 JGI exon 37061 37174 . - . name "fgenesh1_pg.C_chr_1000007"; transcriptId 873 2 | chr_1 JGI CDS 37061 37174 . - 0 name "fgenesh1_pg.C_chr_1000007"; proteinId 873; exonNumber 3 3 | chr_1 JGI exon 37315 37620 . - . name "fgenesh1_pg.C_chr_1000007"; transcriptId 873 4 | chr_1 JGI CDS 37315 37620 . - 0 name "fgenesh1_pg.C_chr_1000007"; proteinId 873; exonNumber 2 5 | chr_1 JGI exon 37752 38216 . - . name "fgenesh1_pg.C_chr_1000007"; transcriptId 873 6 | chr_1 JGI CDS 37752 38216 . - 0 name "fgenesh1_pg.C_chr_1000007"; proteinId 873; exonNumber 1 7 | -------------------------------------------------------------------------------- /gff/Tests/GFF/problem_sequence_region.gff3: -------------------------------------------------------------------------------- 1 | ##gff-version 3 2 | #!gff-spec-version 1.21 3 | #!processor NCBI annotwriter 4 | ##sequence-region 1 2482535 5 | ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1282 6 | 1 Local region 1 2482535 . + . ID=1:1..2482535;Dbxref=taxon:1282;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA 7 | 1 . gene 1 1356 . + . ID=gene-test_000001;Name=dnaA;gbkey=Gene;gene=dnaA;gene_biotype=protein_coding 8 | -------------------------------------------------------------------------------- /gff/Tests/GFF/spaces.gff3: -------------------------------------------------------------------------------- 1 | ##gff-version 3 2 | contig1 . gene 1544 2057 . - . ID=contig1.1 3 | contig1 . mRNA 1544 2057 . - . ID=mRNA.contig1.1;Parent=contig1.1 4 | contig1 . mRNA 1544 2057 . - . foo=bar;ID=mRNA.contig1.1;Parent=contig1.1 5 | contig1 . mRNA 1544 2057 . - . ID=mRNA.contig1.1;Parent=contig1.1; foo=bar 6 | -------------------------------------------------------------------------------- /gff/Tests/GFF/unescaped-semicolon.gff3: -------------------------------------------------------------------------------- 1 | ##gff-version 3 2 | chr1 . gene 1 100 . + . ID=PH01000020G1780;Description="osFTL6 FT-Like6 homologous to Flowering Locus T gene; contains Pfam profile PF01161: Phosphatidylethanolamine-binding protein, expressed" -------------------------------------------------------------------------------- /gff/Tests/GFF/wormbase_gff2_alt.txt: -------------------------------------------------------------------------------- 1 | Remanei_genome Genomic_canonical region 1 7816 . + . Sequence "Contig1020"; 2 | Contig102 WU_MERGED CDS 1629 3377 . - . CDS "cr01.sctg102.wum.2.1" 3 | Contig102 WU_MERGED coding_exon 2927 3377 . - . CDS "cr01.sctg102.wum.2.1" 4 | Contig102 WU_MERGED coding_exon 2474 2875 . - . CDS "cr01.sctg102.wum.2.1" 5 | Contig102 WU_MERGED coding_exon 1928 2430 . - . CDS "cr01.sctg102.wum.2.1" 6 | Contig102 WU_MERGED coding_exon 1629 1883 . - . CDS "cr01.sctg102.wum.2.1" 7 | Contig102 WU_MERGED intron 2876 2926 . - . CDS "cr01.sctg102.wum.2.1" 8 | Contig102 WU_MERGED intron 2431 2473 . - . CDS "cr01.sctg102.wum.2.1" 9 | Contig102 WU_MERGED intron 1884 1927 . - . CDS "cr01.sctg102.wum.2.1" 10 | -------------------------------------------------------------------------------- /gff/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | """Python setup file for Blue Collar Bioinformatics scripts and modules. 3 | """ 4 | from distribute_setup import use_setuptools 5 | use_setuptools() 6 | from setuptools import setup, find_packages 7 | 8 | __version__ = "Undefined" 9 | for line in open('BCBio/GFF/__init__.py'): 10 | if (line.startswith('__version__')): 11 | exec(line.strip()) 12 | 13 | setup(name="bcbio-gff", 14 | version=__version__, 15 | author="Brad Chapman", 16 | author_email="chapmanb@50mail.com", 17 | license="Biopython License", 18 | description="Read and write Generic Feature Format (GFF) with Biopython integration.", 19 | url="https://github.com/chapmanb/bcbb/tree/master/gff", 20 | packages=find_packages(), 21 | install_requires=["six", "biopython"] 22 | ) 23 | -------------------------------------------------------------------------------- /hg38alt/README.md: -------------------------------------------------------------------------------- 1 | # Annotate BED files with hg38 alts 2 | 3 | Helps identify regions in targeted BED files that have alternative haplotypes 4 | in the hg38 build. Intended as an initial step for better determining how to 5 | represent these. 6 | 7 | Input set of regions from the GRC: https://www.ncbi.nlm.nih.gov/grc/human 8 | -------------------------------------------------------------------------------- /keyval_testing/couchdb_get_freqs.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | """Get frequencies from a CouchDB remote database. 3 | 4 | Total time : 14:22.19s 5 | Memory : 8154 6 | Percent CPU : 63.8% 7 | """ 8 | import sys 9 | import random 10 | import couchdb.client 11 | 12 | def main(): 13 | db_name = "reads_090504/read_to_freq" 14 | server = couchdb.client.Server("http://mothra:5984/") 15 | db = server[db_name] 16 | 17 | max_records = 2810717 18 | num_trials = 500000 19 | for index in range(num_trials): 20 | read_id = str(random.randint(0, max_records)) 21 | doc = db[read_id] 22 | freq = int(doc["frequency"]) 23 | if index % 10000 == 0: 24 | print index, read_id, freq 25 | 26 | if __name__ == "__main__": 27 | main() 28 | -------------------------------------------------------------------------------- /keyval_testing/freq_to_tyrant.py: -------------------------------------------------------------------------------- 1 | """Write file of read frequencies to a Tokyo Tyrant server. 2 | 3 | ttserver test.tcb#opts=ld#bnum=1000000#lcnum=10000 4 | 5 | Total time : 11:58.90s 6 | Memory : 2536 7 | Percent CPU : 39.2% 8 | 9 | -rw-r--r-- 1 chapman users 24M 2009-05-07 09:01 test.tcb 10 | """ 11 | import sys 12 | import pytyrant 13 | import json 14 | 15 | def main(in_file): 16 | db = pytyrant.PyTyrant.open("mothra", 1978) 17 | 18 | with open(in_file) as in_handle: 19 | for read_index, freq in enumerate(in_handle): 20 | db[str(read_index)] = json.dumps(dict(frequency=freq)) 21 | 22 | if __name__ == "__main__": 23 | main(sys.argv[1]) 24 | -------------------------------------------------------------------------------- /keyval_testing/tyrant_get_freqs.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | """Get frequencies from a Tokyo Tyrant remote database. 3 | 4 | Total time : 3:20.37s 5 | Memory : 6706 6 | Percent CPU : 35.4% 7 | """ 8 | import sys 9 | import random 10 | import pytyrant 11 | import json 12 | 13 | def main(): 14 | db = pytyrant.PyTyrant.open("mothra", 1978) 15 | 16 | max_records = 2810718 17 | num_trials = 500000 18 | for index in range(num_trials): 19 | read_id = str(random.randint(0, max_records)) 20 | freq = int(json.loads(db[read_id])['frequency']) 21 | if index % 10000 == 0: 22 | print index, freq, read_id 23 | 24 | if __name__ == "__main__": 25 | main() 26 | -------------------------------------------------------------------------------- /nextgen/README.md: -------------------------------------------------------------------------------- 1 | ## bcbio-nextgen 2 | 3 | A python toolkit providing best-practice pipelines for fully automated high 4 | throughput sequencing analysis. 5 | 6 | This project has finally moved into its own top-level repository: 7 | 8 | https://github.com/chapmanb/bcbio-nextgen 9 | 10 | Further development and improvements will happen there so please follow that 11 | repository for the latest updates. If you have a fork of code you'd like to 12 | contribute that is under the old directory structure please let Brad know and we 13 | will work to merge it in. 14 | 15 | -------------------------------------------------------------------------------- /nextgen/bcbio/__init__.py: -------------------------------------------------------------------------------- 1 | """Blue collar bioinformatics main module. 2 | """ 3 | __import__('pkg_resources').declare_namespace(__name__) 4 | -------------------------------------------------------------------------------- /nextgen/bcbio/bam/__init__.py: -------------------------------------------------------------------------------- 1 | """Functionality to query and extract information from aligned BAM files. 2 | """ 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/bam/fastq.py: -------------------------------------------------------------------------------- 1 | from bcbio.log import logger 2 | from bcbio import utils 3 | from Bio import SeqIO 4 | 5 | 6 | @utils.memoize_outfile(stem="groom") 7 | def groom(in_file, in_qual="fastq-sanger", out_dir=None, out_file=None): 8 | """ 9 | Grooms a FASTQ file into sanger format, if it is not already in that 10 | format. Use fastq-illumina for Illumina 1.3-1.7 qualities and 11 | fastq-solexa for the original solexa qualities. When in doubt, your 12 | sequences are probably fastq-sanger. 13 | 14 | """ 15 | if in_qual == "fastq-sanger": 16 | logger.info("%s is already in Sanger format." % (in_file)) 17 | return out_file 18 | 19 | count = SeqIO.convert(in_file, in_qual, out_file, "fastq-sanger") 20 | logger.info("Converted %d reads in %s to %s." % (count, in_file, out_file)) 21 | return out_file 22 | -------------------------------------------------------------------------------- /nextgen/bcbio/distributed/__init__.py: -------------------------------------------------------------------------------- 1 | """Handle distributing processing functionality over multiple machines. 2 | """ 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/galaxy/__init__.py: -------------------------------------------------------------------------------- 1 | """Shared functionality for interacting with Galaxy. 2 | """ 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/hmmer/__init__.py: -------------------------------------------------------------------------------- 1 | """Utilities for dealing with HMMER. 2 | """ 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/ngsalign/__init__.py: -------------------------------------------------------------------------------- 1 | """Functionality to help perform next-gen sequencing alignments. 2 | """ 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/picard/__init__.py: -------------------------------------------------------------------------------- 1 | # Back compatibility -- use broad subdirectory for new code 2 | from bcbio.broad import BroadRunner as PicardRunner 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/picard/metrics.py: -------------------------------------------------------------------------------- 1 | # Back compatibility -- use broad subdirectory for new code 2 | from bcbio.broad.metrics import * 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/picard/utils.py: -------------------------------------------------------------------------------- 1 | # Placeholder for back compatibility. 2 | from bcbio.utils import * 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/pipeline/__init__.py: -------------------------------------------------------------------------------- 1 | """High level code for driving a next-gen analysis pipeline. 2 | 3 | This structures processing steps into the following modules: 4 | 5 | - lane.py: Analyze a single fastq file. 6 | - fastq.py: Utilities to retrieve fastq files from flowcell directories. 7 | - demultiplex.py: Split file by barcodes, if required. 8 | - alignment.py: Align to a reference genome. 9 | 10 | - sample.py: Analyze a sample, which may consist of multiple lanes or 11 | barcoded samples on a lane. 12 | - merge.py: Merge multiple sample files in one processing run. 13 | - variation.py: Calculate SNP/indel variations for a sample. 14 | - qcsummary.py: Quality control, alignment metrics and summary information. 15 | """ 16 | -------------------------------------------------------------------------------- /nextgen/bcbio/rnaseq/__init__.py: -------------------------------------------------------------------------------- 1 | """RNA-seq analysis code for assessing transcript abundance. 2 | """ 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/solexa/__init__.py: -------------------------------------------------------------------------------- 1 | """Manage and automate the Solexa read processing pipeline. 2 | """ 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/structural/__init__.py: -------------------------------------------------------------------------------- 1 | """Detect structural variation in genomes using high-throughput sequencing data. 2 | """ 3 | -------------------------------------------------------------------------------- /nextgen/bcbio/variation/__init__.py: -------------------------------------------------------------------------------- 1 | """Analyze next-gen genomic variation, wrapping the GATK toolkit and other utilities. 2 | """ 3 | -------------------------------------------------------------------------------- /nextgen/config/universe_wsgi.ini: -------------------------------------------------------------------------------- 1 | # Several scripts pull information from Galaxy's standard configuration 2 | # file. The post-processing scripts use the following variables. 3 | 4 | [app:main] 5 | enable_api = True 6 | library_import_dir = /source/galaxy/upload 7 | 8 | [galaxy_amqp] 9 | host = rabbitmq.host.machine 10 | port = 5672 11 | userid = rabbitmq_user 12 | password = rabbitmq_passwd 13 | virtual_host = galaxy_messaging_engine 14 | queue = galaxy_queue 15 | exchange = galaxy_exchange 16 | routing_key = bar_code_scanner 17 | -------------------------------------------------------------------------------- /nextgen/docs/index.rst: -------------------------------------------------------------------------------- 1 | .. bcbio_nextgen documentation master file, created by 2 | sphinx-quickstart on Tue Jan 1 13:33:31 2013. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | bcbio-nextgen 7 | ============= 8 | 9 | A python toolkit providing best-practice pipelines for fully automated 10 | high throughput sequencing analysis. 11 | 12 | Contents: 13 | 14 | .. toctree:: 15 | :maxdepth: 2 16 | 17 | contents/installation 18 | contents/testing 19 | contents/configuration 20 | contents/parallel 21 | contents/internals 22 | 23 | 24 | Indices and tables 25 | ================== 26 | 27 | * :ref:`genindex` 28 | * :ref:`modindex` 29 | * :ref:`search` 30 | 31 | -------------------------------------------------------------------------------- /nextgen/scripts/utils/build_gatk_jar.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | # build a GATK jar without embedded dependencies from current git 3 | mkdir -p ~/tmp/gatkbuild 4 | cd ~/tmp/gatkbuild 5 | git clone https://github.com/broadgsa/gatk.git 6 | cd gatk 7 | ant 8 | cd dist 9 | mkdir -p nodeps 10 | for x in GenomeAnalysisTK.jar Aligner.jar Queue.jar StingUtils.jar vcf.jar picard-private-parts*jar 11 | do 12 | cp $x nodeps 13 | done 14 | cd nodeps 15 | for x in *.jar 16 | do 17 | jar xvf $x 18 | rm -f $x 19 | done 20 | jar cvmf META-INF/MANIFEST.MF ../gatk.jar * 21 | -------------------------------------------------------------------------------- /nextgen/scripts/utils/convert_samplesheet_config.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | """Convert Illumina SampleSheet CSV files to the run_info.yaml input file. 3 | 4 | This allows running the analysis pipeline without Galaxy, using CSV input 5 | files from Illumina SampleSheet or Genesifter. 6 | 7 | Usage: 8 | convert_samplesheet_config.py 9 | """ 10 | import sys 11 | 12 | from bcbio.solexa import samplesheet 13 | 14 | if __name__ == "__main__": 15 | samplesheet.csv2yaml(sys.argv[1]) 16 | -------------------------------------------------------------------------------- /nextgen/tests/bed2interval/test_bed2interval.yaml: -------------------------------------------------------------------------------- 1 | input: tests/data/organisms/mouse/mouse.bam 2 | correct: tests/bed2interval/mouse.interval 3 | 4 | annotation: 5 | bed: tests/data/organisms/mouse/mouse.bed 6 | -------------------------------------------------------------------------------- /nextgen/tests/data/110221_empty_FC12345AAXX/1_110221_FC12345AAXX_fastq.txt: -------------------------------------------------------------------------------- 1 | @HWI-EAS264:1:1:1100:931#0 2 | NCCTGACCTATTTTGTTCACTCTAAGATATCACTCCCTTTGTATTTCCTTGGTGCCTAATGTCACTTGTGTTACTTGAA 3 | + 4 | BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 5 | -------------------------------------------------------------------------------- /nextgen/tests/data/110221_empty_FC12345AAXX/2_110221_FC12345AAXX_fastq.txt: -------------------------------------------------------------------------------- 1 | @HWI-EAS264:2:1:1052:948#0 2 | NAAAACCCATTTATGCCTAGTGTTCCATTATTGGAACGCTAAGCTTGTGGGAATCATATATATCCTACTGCTCTTGTAA 3 | + 4 | BHHJGMJHHJWWXVW_____[Y[Y[______R_W___________BBBBBBBBBBBBBBBBBBBBBBBBBBBWTWWWVX 5 | -------------------------------------------------------------------------------- /nextgen/tests/data/110221_empty_FC12345AAXX/3_110221_FC12345AAXX_fastq.txt: -------------------------------------------------------------------------------- 1 | @HWI-EAS264:2:1:1052:948#0 2 | NAAAACCCATTTATGCCTAGTGTTCCATTATTGGAACGCTAAGCTTGTGGGAATCATATATATCCTACTGCTCTTGTAA 3 | + 4 | BHHJGMJHHJWWXVW_____[Y[Y[______R_W___________BBBBBBBBBBBBBBBBBBBBBBBBBBBWTWWWVX 5 | -------------------------------------------------------------------------------- /nextgen/tests/data/automated/run_info-bam.yaml: -------------------------------------------------------------------------------- 1 | details: 2 | - algorithm: 3 | #aligner: false 4 | #recalibrate: false 5 | #realign: false 6 | aligner: novoalign 7 | variantcaller: gatk 8 | quality_format: Standard 9 | coverage_interval: regional 10 | analysis: variant 11 | description: Test1 12 | genome_build: hg19 13 | lane: 7 14 | files: [7_100326_FC6107FAAXX.bam] 15 | -------------------------------------------------------------------------------- /nextgen/tests/data/automated/run_info-rnaseq.yaml: -------------------------------------------------------------------------------- 1 | fc_date: '110907' 2 | fc_name: ERP000591 3 | details: 4 | - analysis: RNA-seq 5 | algorithm: 6 | quality_format: Standard 7 | description: Test1 8 | genome_build: mm9 9 | lane: 1 10 | -------------------------------------------------------------------------------- /nextgen/tests/data/automated/tool-data/bowtie_indices.loc: -------------------------------------------------------------------------------- 1 | hg19 hg19 hg19 ../../genomes/hg19/bowtie/hg19 2 | mm9 mm9 mm9 ../../genomes/mm9/bowtie/mm9 3 | -------------------------------------------------------------------------------- /nextgen/tests/data/automated/tool-data/bwa_index.loc: -------------------------------------------------------------------------------- 1 | hg19 hg19 hg19 ../../genomes/hg19/bwa/hg19.fa 2 | mm9 mm9 mm9 ../../genomes/mm9/bwa/mm9.fa 3 | -------------------------------------------------------------------------------- /nextgen/tests/data/automated/tool-data/mosaik_index.loc: -------------------------------------------------------------------------------- 1 | hg19 hg19 hg19 ../../genomes/hg19/mosaik/hg19.dat 2 | -------------------------------------------------------------------------------- /nextgen/tests/data/automated/tool-data/sam_fa_indices.loc: -------------------------------------------------------------------------------- 1 | index hg19 ../../genomes/hg19/seq/hg19.fa 2 | index mm9 ../../genomes/mm9/seq/mm9.fa 3 | -------------------------------------------------------------------------------- /nextgen/tests/data/automated/universe_wsgi.ini: -------------------------------------------------------------------------------- 1 | # Several scripts pull information from Galaxy's standard configuration 2 | # file. The post-processing scripts use the following variables. 3 | 4 | [app:main] 5 | enable_api = True 6 | library_import_dir = /source/galaxy/upload 7 | 8 | [galaxy_amqp] 9 | host = localhost 10 | port = 5672 11 | userid = bionextgen 12 | password = tester 13 | -------------------------------------------------------------------------------- /nextgen/tests/data/automated/variant_regions-variantcall.bed: -------------------------------------------------------------------------------- 1 | chrM 100 5000 2 | chr22 1 20000 3 | -------------------------------------------------------------------------------- /nextgen/tests/data/illumina_samplesheet_fcid_mixed.csv: -------------------------------------------------------------------------------- 1 | "FCID","Lane","SampleID","SampleRef","Index","Description","Y","Recipe","Operator" 2 | "69RN3ABXX",4,"6311N_4","a_ref","TGACCA","Test","N","R1","ES" 3 | "12NN4ABXX",5,"8319N_12","a_ref","CTTGTA","Test","N","R1","ES" 4 | "69RN3ABXX",5,"8319T_6","a_ref","GCCAAT","Test","N","R1","ES" 5 | "12NN4ABXX",6,"9161T_6","a_ref","GCCAAT","Test","N","R1","ES" 6 | "69RN3ABXX",6,"9161N_12","a_ref","CTTGTA","Test","N","R1","ES" 7 | "12NN4ABXX",7,"7214N_4","a_ref","TGACCA","Test","N","R1","ES" 8 | "69RN3ABXX",7,"7214T_12","a_ref","CTTGTA","Test","N","R1","ES" 9 | "12NN4ABXX",8,"PhiX_3","PhiX_controllane","TTAGGC","Test","Y","R1","ES" -------------------------------------------------------------------------------- /nextgen/tests/data/organisms/mouse/mouse.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chapmanb/bcbb/320353c64ee0dc938113ca36f19b2e6de6b597be/nextgen/tests/data/organisms/mouse/mouse.bam -------------------------------------------------------------------------------- /nextgen/tests/data/organisms/mouse/mouse.bed: -------------------------------------------------------------------------------- 1 | 17 5410863 5440260 ENSMUST00000005053 0 - 5411368 5440217 0 4 604,138,101,128, 0,22578,28668,29269, 2 | -------------------------------------------------------------------------------- /nextgen/tests/data/run_info-alternatives.yaml: -------------------------------------------------------------------------------- 1 | # Describe various alternatives to specify run information 2 | --- 3 | fc_name: tester 4 | fc_date: 1234 5 | details: 6 | - lane: 1 7 | name: "Standard multiplex" 8 | genome_build: hg19 9 | multiplex: 10 | - barcode_id: 1 11 | barcode_type: "Illumina" 12 | name: "BC1" 13 | sequence: ATCACG 14 | - barcode_id: 2 15 | barcode_type: "Illumina" 16 | name: "BC2" 17 | sequence: CGATGT 18 | - lane: 1 19 | name: "Single barcode" 20 | genome_build: mm9 21 | barcode: 22 | barcode_id: 3 23 | barcode_type: "Illumina" 24 | sequence: TTAGGC 25 | - lane: 2 26 | name: "No barcode" 27 | genome_build: hg18 28 | 29 | -------------------------------------------------------------------------------- /nextgen/tests/data/structural/NA12878-hydra.txt: -------------------------------------------------------------------------------- 1 | chr22 9763 9934 chr22 10111 10213 1 4 + + 0 3 1 1 451 4 4 4 4 4 0 0 2 | chr22 7763 7934 chr22 12111 12213 2 4 + - 0 3 1 1 451 4 4 4 4 4 0 0 3 | chr22 8763 8934 chr22 11111 11213 3 4 - - 0 3 1 1 451 4 4 4 4 4 0 0 4 | chr22 9763 9934 chr22 13111 13213 4 4 - + 0 3 1 1 451 4 4 4 4 4 0 0 5 | -------------------------------------------------------------------------------- /nextgen/tests/split_vcf/test_split_vcf.yaml: -------------------------------------------------------------------------------- 1 | input_split: tests/split_vcf/data/NA12878-hydra.vcf 2 | correct_split: 3 | - tests/split_vcf/data/chrM_correct.vcf 4 | - tests/split_vcf/data/chr22_correct.vcf 5 | 6 | ref: 7 | fasta: tests/data/genomes/hg19/seq/hg19.fa 8 | 9 | program: 10 | samtools: samtools 11 | -------------------------------------------------------------------------------- /nextgen/tests/test_fastq.py: -------------------------------------------------------------------------------- 1 | import unittest 2 | import tempfile 3 | from bcbio.bam.fastq import groom 4 | from bcbio.utils import locate, file_exists 5 | import os 6 | import tempfile 7 | 8 | 9 | class Fastq(unittest.TestCase): 10 | 11 | def setUp(self): 12 | self.root_dir = os.path.join(__file__, "data/fastq/") 13 | 14 | def test_groom(self): 15 | illumina_dir = os.path.join(self.root_dir, "illumina") 16 | test_data = locate("*.fastq", illumina_dir) 17 | sanger_dir = tempfile.mkdtemp() 18 | out_files = [groom(x, in_qual="fastq-illumina", out_dir=sanger_dir) for 19 | x in test_data] 20 | self.assertTrue(all(map(file_exists, out_files))) 21 | -------------------------------------------------------------------------------- /papers/bcbio-nextgen/Makefile: -------------------------------------------------------------------------------- 1 | all: clean chapman_bcbio.bib 2 | pdflatex chapman_bcbio.tex 3 | bibtex chapman_bcbio 4 | pdflatex chapman_bcbio.tex 5 | pdflatex chapman_bcbio.tex 6 | 7 | chapman_bcbio.bib: 8 | python fix_bibfile.py bcbio-nextgen.bib chapman_bcbio.bib 9 | 10 | clean: 11 | rm -f chapman_bcbio.aux 12 | rm -f chapman_bcbio.bbl 13 | rm -f chapman_bcbio.blg 14 | rm -f chapman_bcbio.log 15 | 16 | -------------------------------------------------------------------------------- /papers/bcbio-nextgen/chapman_bcbio.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chapmanb/bcbb/320353c64ee0dc938113ca36f19b2e6de6b597be/papers/bcbio-nextgen/chapman_bcbio.pdf -------------------------------------------------------------------------------- /papers/bcbio-nextgen/fix_bibfile.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | in_file, out_file = sys.argv[1:] 4 | 5 | with open(in_file) as in_handle: 6 | with open(out_file, "w") as out_handle: 7 | for line in in_handle: 8 | if line.strip().startswith("language"): 9 | line = None 10 | elif line.strip().startswith("@misc"): 11 | base, cite = line.split("{") 12 | cite_parts = [x.strip() for x in cite.split("_") if x.strip()] 13 | line = base + "{" + cite_parts[0] + ",\n" 14 | if line: 15 | out_handle.write(line) 16 | -------------------------------------------------------------------------------- /papers/bcbio-nextgen/parallel-genome.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chapmanb/bcbb/320353c64ee0dc938113ca36f19b2e6de6b597be/papers/bcbio-nextgen/parallel-genome.png -------------------------------------------------------------------------------- /papers/bcbio-nextgen/validation-gatkprep.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/chapmanb/bcbb/320353c64ee0dc938113ca36f19b2e6de6b597be/papers/bcbio-nextgen/validation-gatkprep.png 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-------------------------------------------------------------------------------- 1 | Small utility scripts and plotting to support evaluation of quality 2 | binning (40 quality values to 8) on alignment and variant calling 3 | -------------------------------------------------------------------------------- /qualbin/qualbin_discordant_check.yaml: -------------------------------------------------------------------------------- 1 | dir: 2 | discordant: /usr/local/projects/CLIA-Validation/secondary/qualbin/compare 3 | replicate: /usr/local/projects/CLIA-Validation/secondary/variants/work/ensemble/compare/gatk 4 | orig: /usr/local/projects/CLIA-Validation/secondary/qualbin/work/gatk 5 | orig: 6 | std: 1_130209_qualbin-sort-dup-gatkrecal-realign-variants-combined-phased-effects.vcf 7 | prebin: 2_130209_qualbin-sort-dup-gatkrecal-realign-variants-combined-phased-effects.vcf 8 | allbin: 3_130209_qualbin-sort-dup-gatkrecal-realign-variants-combined-phased-effects.vcf 9 | 10 | -------------------------------------------------------------------------------- /semantic/sparta_ex.py: -------------------------------------------------------------------------------- 1 | import urllib 2 | from rdflib import ConjunctiveGraph as Graph 3 | import sparta 4 | 5 | url = 'http://www.gopubmed.org/GoMeshPubMed/gomeshpubmed/Search/RDF?q=18463287&type=RdfExportAll' 6 | gopubmed_handle = urllib.urlopen(url) 7 | graph = Graph() 8 | graph.parse(gopubmed_handle) 9 | gopubmed_handle.close() 10 | 11 | graph_subjects = list(set(graph.subjects())) 12 | sparta_factory = sparta.ThingFactory(graph) 13 | for subject in graph_subjects: 14 | sparta_graph = sparta_factory(subject) 15 | print subject, [unicode(i) for i in sparta_graph.dc_title][0] 16 | -------------------------------------------------------------------------------- /stats/diffexp_example-diffs.csv: -------------------------------------------------------------------------------- 1 | Region,Condition 1 count,Condition 2 count,edgeR p-value 2 | GeneC,100,25,1.05987026716e-18 3 | GeneA,15,60,0.000606472874173 4 | GeneD,20,20,0.281371046659 5 | GeneB,20,30,0.999999999999 6 | -------------------------------------------------------------------------------- /stats/diffexp_example-go_map.txt: -------------------------------------------------------------------------------- 1 | GeneA GO:0042578 2 | GeneC GO:0016791 3 | GeneB GO:0016298 4 | GeneD GO:0016298 5 | -------------------------------------------------------------------------------- /stats/diffexp_example.csv: -------------------------------------------------------------------------------- 1 | Region,Condition 1,Condition 2 2 | Total,1000,1500 3 | GeneA,15,60 4 | GeneB,20,30 5 | GeneC,100,25 6 | GeneD,20,20 7 | GeneE,0,0 8 | -------------------------------------------------------------------------------- /talks/2015_iowast_career/chapman_career.pdf: -------------------------------------------------------------------------------- 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union11callableonlymerged_nouncert_addcert_excludesimplerep_excludesegdups_v2.13.bed 13 | ref: Hsapiens/GRCh37/seq/GRCh37.fa 14 | subset: 15 | name: NA12878-nist-v2_13-NGv3 16 | interval: NGv3.bed -------------------------------------------------------------------------------- /validation/README.md: -------------------------------------------------------------------------------- 1 | Scripts to support grading and validation of variant calling pipelines against 2 | NIST NA12878 reference materials. 3 | -------------------------------------------------------------------------------- /validation/pull_bwa_novoalign_diffs.yaml: -------------------------------------------------------------------------------- 1 | dirs: 2 | work: postanalysis/aligners 3 | ref: /cm/shared/apps/harvard/genomes/Hsapiens/GRCh37/seq/GRCh37.fa 4 | calls: 5 | bwa: validate/NA12878-2/gatk/work/NA12878-2-ref-eval-concordance.vcf 6 | bwa-orig: gatk/2_2013-04-03_methodcmp-sort-variants-combined-effects.vcf 7 | novoalign: validate/NA12878-1/gatk/work/NA12878-1-ref-eval-concordance.vcf 8 | callable: 9 | novoalign: align/NA12878-1/1_2013-04-03_methodcmp-sort-callable_sample.bed -------------------------------------------------------------------------------- /validation/pull_shared_discordants.yaml: -------------------------------------------------------------------------------- 1 | dirs: 2 | work: postanalysis/refmaterials 3 | ref: /cm/shared/apps/harvard/genomes/Hsapiens/GRCh37/seq/GRCh37.fa 4 | calls: 5 | gatk: validate/NA12878-2/gatk/work/NA12878-2-eval-ref-discordance-annotate.vcf 6 | freebayes: validate/NA12878-2/freebayes/work/NA12878-2-eval-ref-discordance-annotate.vcf 7 | gatk-haplotype: validate/NA12878-2/gatk-haplotype/work/NA12878-2-eval-ref-discordance-annotate.vcf --------------------------------------------------------------------------------