{"id":23768542,"url":"https://github.com/nci-gdc/variant-filtration-tool","last_synced_at":"2025-09-05T13:31:05.535Z","repository":{"id":50087347,"uuid":"56620852","full_name":"NCI-GDC/variant-filtration-tool","owner":"NCI-GDC","description":"Support tools for the GDC Variant Filtration Workflow","archived":false,"fork":false,"pushed_at":"2025-06-20T19:48:47.000Z","size":193,"stargazers_count":1,"open_issues_count":4,"forks_count":2,"subscribers_count":8,"default_branch":"main","last_synced_at":"2025-06-20T20:49:21.132Z","etag":null,"topics":["bioinformatics","docker","workflow-tool"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NCI-GDC.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2016-04-19T18:20:02.000Z","updated_at":"2025-04-03T16:01:11.000Z","dependencies_parsed_at":"2022-08-27T03:19:09.767Z","dependency_job_id":"36546a5e-a2fb-404a-90ea-11b9f05416c9","html_url":"https://github.com/NCI-GDC/variant-filtration-tool","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/NCI-GDC/variant-filtration-tool","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fvariant-filtration-tool","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fvariant-filtration-tool/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fvariant-filtration-tool/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fvariant-filtration-tool/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NCI-GDC","download_url":"https://codeload.github.com/NCI-GDC/variant-filtration-tool/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCI-GDC%2Fvariant-filtration-tool/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273765498,"owners_count":25164144,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-05T02:00:09.113Z","response_time":402,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","docker","workflow-tool"],"created_at":"2025-01-01T01:37:23.515Z","updated_at":"2025-09-05T13:31:05.492Z","avatar_url":"https://github.com/NCI-GDC.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"GDC Variant Filtration Tool\n---\n\nThis repository contains the source code used in the VCF variant filtration\nworkflows within the GDC. A single CLI is generated with multiple subcommands. \n\n## Requirements \n\n* Python \u003e= 3.6\n* pysam\n* defopt\n \n## Subcommands \n\n### `add-oxog-filters`\n\nAdds 'oxog' filter tag to VCFs.\n\n```\nusage: gdc-filtration-tools add-oxog-filters [-h]\n                                             input_vcf input_dtoxog output_vcf\n\nAdds 'oxog' filter tag to VCFs.\n\npositional arguments:\n  input_vcf     The full input VCF file to filter.\n  input_dtoxog  The dtoxog VCF from dtoxog-maf-to-vcf used to annotate the full input VCF.\n  output_vcf    The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.\n\noptional arguments:\n  -h, --help    show this help message and exit\n```\n\n### `create-dtoxog-maf`\n\nTakes a SNP-only VCF file and converts it to the dToxoG MAF format\nwhich includes the OXOQ value.\n\n```\nusage: gdc-filtration-tools create-dtoxog-maf [-h]\n                                              input_vcf output_file reference\n                                              oxog_file oxoq_score\n\nTakes a SNP-only VCF file and converts it to the dToxoG MAF format\nwhich includes the OXOQ value.\n\npositional arguments:\n  input_vcf    The input SNP-only VCF file to convert to dToxoG MAF.\n  output_file  The output MAF file to create.\n  reference    Faidx indexed reference fasta file.\n  oxog_file    Metrics file output from GATK OxoGMetrics tool.\n  oxoq_score   The oxoQ score.\n\noptional arguments:\n  -h, --help   show this help message and exit\n```\n\n### `create-oxog-intervals`\n\nTakes a SNP-only VCF file and creates an interval list for\nuse by the Broad oxog metrics tool.\n\n```\nusage: gdc-filtration-tools create-oxog-intervals [-h] input_vcf output_file\n\nTakes a SNP-only VCF file and creates an interval list for\nuse by the Broad oxog metrics tool.\n\npositional arguments:\n  input_vcf    The input SNP-only VCF file to extract intervals from.\n  output_file  The output interval list to create.\n\noptional arguments:\n  -h, --help   show this help message and exit\n```\n\n### `dtoxog-maf-to-vcf`\n\nTransforms dToxoG MAF to minimal VCF of only dtoxo failures.\n\n```\nusage: gdc-filtration-tools dtoxog-maf-to-vcf [-h]\n                                              input_maf reference_fa\n                                              output_vcf\n\nTransforms dToxoG MAF to minimal VCF of only dtoxo failures.\n\npositional arguments:\n  input_maf     The annotated dtoxog MAF output file.\n  reference_fa  Reference fasta used to make seqdict header.\n  output_vcf    The output minimal VCF with only failed dtoxog records. BGzip and tabix-index created if ends with '.gz'.\n\noptional arguments:\n  -h, --help    show this help message and exit\n```\n\n### `extract-oxoq-from-sqlite`\n\nExtract the OXOQ score for a particular context from the GDC\nharmonization metrics SQLite file. The score is printed to\nstdout.\n\n```\nusage: gdc-filtration-tools extract-oxoq-from-sqlite [-h] [-c CONTEXT]\n                                                     [-t TABLE]\n                                                     [-i INPUT_STATE]\n                                                     db_file\n\nExtract the OXOQ score for a particular context from the GDC\nharmonization metrics SQLite file. The score is printed to\nstdout.\n\npositional arguments:\n  db_file               Path to the SQLite db file.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -c CONTEXT, --context CONTEXT\n                        The nucleotide context of interest.\n                        (default: CCG)\n  -t TABLE, --table TABLE\n                        The SQLite table name.\n                        (default: picard_CollectOxoGMetrics)\n  -i INPUT_STATE, --input-state INPUT_STATE\n                        The input state to select for in the input_state column.\n                        (default: markduplicates_readgroups)\n```\n\n### `filter-contigs`\n\nFilter out VCF records on chromosomes that are not present\nin the contig lines of the VCF header.\n\n```\nusage: gdc-filtration-tools filter-contigs [-h] input_vcf output_vcf\n\nFilter out VCF records on chromosomes that are not present\nin the contig lines of the VCF header.\n\npositional arguments:\n  input_vcf   The input VCF file to filter.\n  output_vcf  The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.\n\noptional arguments:\n  -h, --help  show this help message and exit\n```\n\n### `filter-nonstandard-variants`\n\nRemove non-ACTG loci from a SNP-ONLY VCF. No validation that\nthe VCF is SNP-only is done.\n\n```\nusage: gdc-filtration-tools filter-nonstandard-variants [-h]\n                                                        input_vcf output_vcf\n\nRemove non-ACTG loci from a SNP-ONLY VCF. No validation that\nthe VCF is SNP-only is done.\n\npositional arguments:\n  input_vcf   The input SNP-only VCF file to filter.\n  output_vcf  The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.\n\noptional arguments:\n  -h, --help  show this help message and exit\n```\n\n### `filter-somatic-score`\n\nFilters SomaticSniper VCF files based on the Somatic Score.\n\n```\nusage: gdc-filtration-tools filter-somatic-score [-h] [-t TUMOR_SAMPLE_NAME]\n                                                 [-d DROP_SOMATIC_SCORE]\n                                                 [-m MIN_SOMATIC_SCORE]\n                                                 input_vcf output_vcf\n\nFilters SomaticSniper VCF files based on the Somatic Score.\n\npositional arguments:\n  input_vcf             The input VCF file to filter.\n  output_vcf            The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -t TUMOR_SAMPLE_NAME, --tumor-sample-name TUMOR_SAMPLE_NAME\n                        The name of the tumor sample in the VCF.\n                        (default: TUMOR)\n  -d DROP_SOMATIC_SCORE, --drop-somatic-score DROP_SOMATIC_SCORE\n                        If the somatic score is \u003c this, remove it.\n                        (default: 25)\n  -m MIN_SOMATIC_SCORE, --min-somatic-score MIN_SOMATIC_SCORE\n                        If the somatic score is \u003e drop_somatic_score and \u003c this value, add ssc filter tag.\n                        (default: 40)\n```\n\n### `format-gdc-vcf`\n\nAdds VCF header metadata specific to the GDC.\n\n```\nusage: gdc-filtration-tools format-gdc-vcf [-h] [-r REFERENCE_NAME]\n                                           input_vcf output_vcf\n                                           patient_barcode case_id\n                                           tumor_barcode tumor_aliquot_uuid\n                                           tumor_bam_uuid normal_barcode\n                                           normal_aliquot_uuid normal_bam_uuid\n\nAdds VCF header metadata specific to the GDC.\n\npositional arguments:\n  input_vcf             The input VCF file to format.\n  output_vcf            The output formatted VCF file to create. BGzip and tabix-index created if ends with '.gz'.\n  patient_barcode       The case submitter id.\n  case_id               The case uuid.\n  tumor_barcode         The tumor aliquot submitter id.\n  tumor_aliquot_uuid    The tumor aliquot uuid.\n  tumor_bam_uuid        The tumor bam uuid.\n  normal_barcode        The normal aliquot submitter id.\n  normal_aliquot_uuid   The normal aliquot uuid.\n  normal_bam_uuid       The normal bam uuid.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -r REFERENCE_NAME, --reference-name REFERENCE_NAME\n                        Reference name to use in header.\n                        (default: GRCh38.d1.vd1.fa)\n```\n\n### `format-pindel-vcf`\n\nFormats Pindel VCFs to work better with GDC downstream workflows.\n\n```\nusage: gdc-filtration-tools format-pindel-vcf [-h] input_vcf output_vcf\n\nFormats Pindel VCFs to work better with GDC downstream workflows.\n\npositional arguments:\n  input_vcf   The input VCF file to filter.\n  output_vcf  The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.\n\noptional arguments:\n  -h, --help  show this help message and exit\n```\n\n### `format-sanger-pindel-vcf`\n\nFormats the Sanger Pindel VCF by filling in the `./.` genotypes to `0/0` for normal and\n`0/1` for tumor.\n\n```\nusage: gdc_filtration_tools format-sanger-pindel-vcf [-h] input_vcf output_vcf\n\nFormats Sanger Pindel VCFs to work better with GDC downstream workflows.\n\npositional arguments:\n  input_vcf   The input VCF file to format.\n  output_vcf  The output formatted VCF file to create. BGzip and tabix-index created if ends with '.gz'.\n\noptional arguments:\n  -h, --help  show this help message and exit\n```\n\n### `position-filter-dkfz`\n\nRemoves VCF records where the POS-2 is less than 0 which\nwill cause an Exception to be thrown in DKFZBiasFilter. We\nassume that the input VCF only contains SNPs, but no assertions\nare made to validate this.\n\n```\nusage: gdc-filtration-tools position-filter-dkfz [-h] input_vcf output_vcf\n\nRemoves VCF records where the POS-2 is less than 0 which\nwill cause an Exception to be thrown in DKFZBiasFilter. We\nassume that the input VCF only contains SNPs, but no assertions\nare made to validate this.\n\npositional arguments:\n  input_vcf   The input VCF file to filter.\n  output_vcf  The output filtered VCF file to create. BGzip and tabix-index created if ends with '.gz'.\n\noptional arguments:\n  -h, --help  show this help message and exit\n```\n\n## Docker Tools\n\n**variant-filtration-tool** \u003cbr /\u003e\nRepository: https://quay.io/ncigdc/variant-filtration-tool \u003cbr /\u003e\nPull by docker.osdc.io/ncigdc/variant-filtration-tool:build-80-ead70e7d\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnci-gdc%2Fvariant-filtration-tool","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnci-gdc%2Fvariant-filtration-tool","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnci-gdc%2Fvariant-filtration-tool/lists"}