├── .dockstore.yml ├── .github └── workflows │ ├── github_release.yml │ └── validate_wdl.yml ├── .gitignore ├── LICENSE ├── README.md ├── dockerfiles ├── BWA │ └── Dockerfile ├── BcfTools │ ├── BcfToolsWithPython │ │ └── Dockerfile │ └── Dockerfile ├── BioBamBam2.0.106 │ └── Dockerfile ├── BioBamBam2.0.73 │ └── Dockerfile ├── CNV │ ├── Dockerfile │ ├── R3.6.1 │ │ ├── Dockerfile │ │ ├── Rscripts │ │ │ ├── CNV_analysis.r │ │ │ ├── find_failed_samples.r │ │ │ ├── modal_CNVs.sh │ │ │ ├── modal_CNVs_vobs.sh │ │ │ ├── modal_cnv.r │ │ │ ├── plotting_functions.r │ │ │ ├── target_regions_analysis.r │ │ │ ├── target_regions_analysis.sh │ │ │ ├── target_regions_analysis_old.r │ │ │ ├── target_regions_analysis_old.sh │ │ │ └── target_regions_analysis_vobs.sh │ │ ├── docker_build.sh │ │ └── installRDeps.R │ ├── docker_build.sh │ ├── docker_versions.tsv │ ├── requirements.txt │ ├── requirements_conda.yml │ └── scripts │ │ ├── HMM_process.py │ │ ├── SSFA.py │ │ ├── breakpoint_detector.py │ │ ├── calculate_median_coverage_by_GC.py │ │ ├── calculate_windowed_accessibility.sh │ │ ├── calculate_windowed_mean_accessibility.py │ │ ├── changes_from_phase2_method.txt │ │ ├── counts_for_HMM.py │ │ ├── coverage_CNVs.sh │ │ ├── coverage_CNVs_vobs.sh │ │ ├── coverage_HMM.sh │ │ ├── coverage_HMM_vobs.sh │ │ ├── get_coverage_stats_by_sample_set.sh │ │ ├── get_coverage_stats_by_sample_set_vobs.sh │ │ ├── get_diagnostic_reads.sh │ │ ├── get_prop_mapq0.py │ │ ├── get_windowed_coverage.sh │ │ ├── get_windowed_coverage_and_diagnostic_reads.sh │ │ ├── indexwrapper.sh │ │ ├── join_CNV_output_files.sh │ │ ├── join_CNV_output_files_vobs.sh │ │ ├── join_gambiae_arabiensis_coverage_variance_files.sh │ │ ├── join_species_coverage_variance_files_vobs.sh │ │ ├── setup_folder.sh │ │ ├── setup_folder_gsutil.sh │ │ ├── setup_folder_gsutil_nobams.sh │ │ ├── setup_folder_gsutil_nobams_wrapper.sh │ │ └── setup_folder_gsutil_wrapper.sh ├── CohortVcfToZarr │ ├── Dockerfile │ ├── cohort_vcf_to_zarr.py │ ├── fixture │ │ └── phased.vcf │ ├── requirements.txt │ └── test_cohort_vcf_to_zarr.py ├── GATK │ └── Dockerfile ├── Import │ └── Dockerfile ├── Lftp │ └── Dockerfile ├── Picard │ └── Dockerfile ├── README.md ├── SampleSelectVariants │ ├── Dockerfile │ ├── fixture │ │ ├── expected.vcf │ │ ├── sample_genotypes.zarr.zip │ │ ├── sites_called.zarr.zip │ │ └── sites_selected.zarr.zip │ ├── requirements.txt │ ├── sample_select_variants.py │ └── test_sample_select_variants.py ├── SampleVcfToZarr │ ├── Dockerfile │ ├── fixture │ │ ├── example.vcf.gz │ │ └── example.vcf.gz.tbi │ ├── requirements.txt │ ├── sample_vcf_to_zarr.py │ └── test_sample_vcf_to_zarr.py ├── Samtools │ └── Dockerfile ├── Shapeit4 │ └── Dockerfile ├── WhatsHap │ └── Dockerfile └── amplicon-parasite-tools │ └── Dockerfile ├── docs ├── RunningAPipeline.md └── specs │ ├── README.md │ ├── cnv-vector.md │ ├── phasing-vector.md │ ├── short-read-alignment-vector.md │ └── snp-genotyping-vector.md ├── pipelines ├── README.md ├── SNP-genotyping-vector │ ├── README.md │ ├── farm5 │ │ ├── SNPGenotyping.options.json │ │ ├── SNPGenotyping.wdl │ │ └── input_files │ │ │ └── small │ │ │ └── AV0148-C.json │ └── gcp │ │ ├── SNPGenotyping.options.json │ │ ├── SNPGenotyping.wdl │ │ └── input_files │ │ └── small │ │ └── AV0148-C.json ├── amplicon-snp-calling-parasite │ ├── AmpliconSNPCallingParasite.wdl │ └── input_files │ │ └── RCN15267.json ├── batch-import-short-read-alignment-and-genotyping-vector │ ├── README.md │ └── farm5 │ │ ├── BatchImportShortReadAlignmentAndGenotyping.options.json │ │ ├── BatchImportShortReadAlignmentAndGenotyping.wdl │ │ └── input_files │ │ ├── small │ │ ├── batch_sample_size_2_lanelets.tsv │ │ └── batch_size2.json │ │ └── validation │ │ ├── 1177-VO-ML-LEHMANN-VMF00015_wgs_lanelets.tsv │ │ ├── batch_size10_validation.json │ │ └── batch_size28_ag3.2_validation.json ├── copy-number-variation-vector │ └── gcp │ │ ├── CNV.wdl │ │ ├── CNVCoverageCalls.wdl │ │ ├── CNVTasks.wdl │ │ ├── HMM.wdl │ │ └── TargetRegions.wdl ├── import-short-read-alignment-vector │ ├── README.md │ └── farm5 │ │ ├── ImportShortReadAlignment.options.json │ │ └── ImportShortReadAlignment.wdl ├── import-short-read-lanelet-alignment-vector │ ├── README.md │ └── farm5 │ │ ├── ImportShortReadLaneletAlignment.options.json │ │ └── ImportShortReadLaneletAlignment.wdl ├── phasing-vector │ ├── README.md │ ├── farm5 │ │ ├── Phasing.wdl │ │ ├── ReadBackedPhasing.options.json │ │ ├── ReadBackedPhasing.wdl │ │ ├── StatisticalPhasing.options.json │ │ ├── StatisticalPhasing.wdl │ │ └── input_files │ │ │ └── small │ │ │ ├── AV0079-C.json │ │ │ ├── AV0148-C.json │ │ │ └── StatisticalPhasing_Small.json │ └── gcp │ │ ├── Phasing.options.json │ │ ├── Phasing.wdl │ │ ├── ReadBackedPhasing.options.json │ │ ├── ReadBackedPhasing.wdl │ │ ├── StatisticalPhasing.options.json │ │ ├── StatisticalPhasing.wdl │ │ └── input_files │ │ ├── Ag1000Phase2_BurkinaFaso.json │ │ ├── Ag1000Phase2_BurkinaFaso_Small.json │ │ ├── Ag1000Phase2_BurkinaFaso_half.json │ │ ├── small │ │ ├── AV0079-C.json │ │ ├── AV0148-C.json │ │ └── StatisticalPhasing_Small.json │ │ └── validation │ │ ├── Phasing_Validation.json │ │ ├── ReadBackedPhasing_AA0052-C.json │ │ ├── ReadBackedPhasing_AB0252-C.json │ │ ├── ReadBackedPhasing_AC0010-C.json │ │ ├── ReadBackedPhasing_BL0358-C.json │ │ └── StatisticalPhasing_Validation.json ├── short-read-alignment-and-genotyping-vector │ ├── README.md │ ├── farm5 │ │ ├── ShortReadAlignmentAndGenotyping.options.json │ │ ├── ShortReadAlignmentAndGenotyping.wdl │ │ └── input_files │ │ │ ├── small │ │ │ ├── AV0079-C.json │ │ │ └── AV0148-C.json │ │ │ └── validation │ │ │ ├── AA0052-C.json │ │ │ ├── AB0252-C.json │ │ │ ├── AC0010-C.json │ │ │ ├── AJ0037-C.json │ │ │ ├── AN0131-C.json │ │ │ ├── AN0280-Cx.json │ │ │ ├── AN0326-C.json │ │ │ ├── AR0078-C.json │ │ │ ├── AZ0156-C.json │ │ │ ├── BL0358-C.json │ │ │ └── validation_lanelets_farm5_local.tsv │ └── gcp │ │ ├── ShortReadAlignmentAndGenotyping.options.json │ │ ├── ShortReadAlignmentAndGenotyping.wdl │ │ └── input_files │ │ ├── small │ │ ├── AV0079-C.json │ │ └── AV0148-C.json │ │ └── validation │ │ ├── AA0052-C.json │ │ ├── AB0252-C.json │ │ ├── AC0010-C.json │ │ ├── AJ0037-C.json │ │ ├── AN0131-C.json │ │ ├── AN0280-Cx.json │ │ ├── AN0326-C.json │ │ ├── AR0078-C.json │ │ ├── AZ0156-C.json │ │ └── BL0358-C.json ├── short-read-alignment-vector │ ├── README.md │ ├── farm5 │ │ ├── ShortReadAlignment.options.json │ │ ├── ShortReadAlignment.wdl │ │ └── input_files │ │ │ ├── AB0252-C.json │ │ │ ├── AN0131-C.json │ │ │ └── small │ │ │ ├── AV0079-C.json │ │ │ └── AV0148-C.json │ ├── fixtures │ │ └── ag1000g-phase3-minimal │ │ │ ├── expected_outputs.tsv │ │ │ └── lanelets.tsv │ └── gcp │ │ ├── ShortReadAlignment.options.json │ │ ├── ShortReadAlignment.wdl │ │ └── input_files │ │ ├── AB0252-C.json │ │ ├── AN0131-C.json │ │ └── small │ │ ├── AV0079-C.json │ │ └── AV0148-C.json └── snp-genotyping-vector │ └── fixtures │ └── ag1000g-phase3-validation │ ├── README.md │ └── lanelets.tsv ├── scripts ├── .gitignore ├── README.md ├── build_pipeline_release.sh ├── create_interval_lists.py ├── sample_select_variants │ ├── .gitignore │ ├── fixture │ │ ├── expected.vcf │ │ ├── sample_genotypes.zarr.zip │ │ ├── sites_called.zarr.zip │ │ └── sites_selected.zarr.zip │ ├── requirements.txt │ ├── sample_select_variants.py │ └── test_sample_select_variants.py ├── validate_wdls.sh └── vector_genotype_concordance │ ├── .gitignore │ ├── README.md │ ├── fixture │ ├── S1.output.categories.tsv │ ├── S1.output.chromosomes.tsv │ ├── S1.output.count.tsv │ ├── S1.output.samples.tsv │ ├── S1.output.totals.tsv │ └── expected.S1.count.tsv │ ├── scripts │ └── vector_genotype_concordance.py │ ├── setup.py │ └── tests │ ├── test_script.py │ └── test_vector_genotype_concordance.py ├── structs ├── README.md ├── ReferenceSequence.wdl ├── farm5 │ └── RunTimeSettings.wdl └── gcp │ └── RunTimeSettings.wdl └── tasks ├── 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