├── .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 ├── 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