{"id":44278173,"url":"https://github.com/msk-access/chip-var","last_synced_at":"2026-02-10T21:14:51.822Z","repository":{"id":99142608,"uuid":"560111695","full_name":"msk-access/chip-var","owner":"msk-access","description":"Workflow for calling and annotating CHIP variants","archived":false,"fork":false,"pushed_at":"2024-10-21T17:54:59.000Z","size":900,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-10-22T08:23:16.886Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://cmo-ci.gitbook.io/chip-variant-calling-and-processing/","language":"Common Workflow Language","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"agpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/msk-access.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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}},"created_at":"2022-10-31T19:01:54.000Z","updated_at":"2024-10-21T17:54:09.000Z","dependencies_parsed_at":"2024-02-07T17:53:57.063Z","dependency_job_id":"8c0d5047-2754-4c5d-b607-905a109139d2","html_url":"https://github.com/msk-access/chip-var","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/msk-access/chip-var","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/msk-access%2Fchip-var","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/msk-access%2Fchip-var/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/msk-access%2Fchip-var/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/msk-access%2Fchip-var/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/msk-access","download_url":"https://codeload.github.com/msk-access/chip-var/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/msk-access%2Fchip-var/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29316959,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-10T20:44:44.282Z","status":"ssl_error","status_checked_at":"2026-02-10T20:44:43.393Z","response_time":65,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2026-02-10T21:14:50.520Z","updated_at":"2026-02-10T21:14:51.808Z","avatar_url":"https://github.com/msk-access.png","language":"Common Workflow Language","funding_links":[],"categories":[],"sub_categories":[],"readme":"# chip-var\nThis is a workflow for calling and annotating CHIP variants. \nThe workflow calls the variants from the BAM file using vardict, which are then filtered based on the simple sample filtering criteria. The filtered variants are then processed, by sorting and normalizing and concating the complex and normal variants into a single VCF file. The concated variants are annotated with COSMIC prevalence counts and converted from VCF to MAF file format. \n\nFor detailed documentation refer to https://cmo-ci.gitbook.io/chip-variant-calling-and-processing/\n\n### Workflows used\n\n- [vardict workflow](https://msk-access.gitbook.io/subworkflows/)\n- [bcftools tabix](https://msk-access.gitbook.io/command-line-tools-cwl/bcftools_1.15.1/)\n- [bcftools norm](https://msk-access.gitbook.io/command-line-tools-cwl/bcftools_1.15.1/)\n- [bcftools sort](https://msk-access.gitbook.io/command-line-tools-cwl/bcftools_1.15.1/)\n- [snpift](https://msk-access.gitbook.io/command-line-tools-cwl/snpsift_annotate_5.0/)\n- [vcf2maf](https://msk-access.gitbook.io/command-line-tools-cwl/vcf2maf_1.6.21/)\n- [maf_annotated_by_bed](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/)\n- [maf_annotated_by_tsv](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_annotated_by_tsv/)\n- [maf_filter_cmoch](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_filter_cmoch/)\n- [maf_tag_cmoch](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.3/maf_tag_cmoch/)\n\n#### Usage\n\n```shell\nusage: chip-var.cwl [-h] --reference_fasta REFERENCE_FASTA --input_bam_case INPUT_BAM_CASE\n                    [--bedfile BEDFILE] --sample_name SAMPLE_NAME\n                    [--vardict_allele_frequency_threshold VARDICT_ALLELE_FREQUENCY_THRESHOLD]\n                    [--retain_info RETAIN_INFO] --concat_output_name CONCAT_OUTPUT_NAME\n                    [--vardict_output_vcf_name VARDICT_OUTPUT_VCF_NAME]\n                    --input_cosmicprevalenceDB_vcf INPUT_COSMICPREVALENCEDB_VCF\n                    --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF\n                    [--snpsift_prevalOpName SNPSIFT_PREVALOPNAME]\n                    [--snpsift_countOpName SNPSIFT_COUNTOPNAME] --input_complexity_bed\n                    INPUT_COMPLEXITY_BED\n                    [--output_complexity_filename OUTPUT_COMPLEXITY_FILENAME]\n                    [--column_name_complexity COLUMN_NAME_COMPLEXITY] --oncoKbApiToken\n                    ONCOKBAPITOKEN --opOncoKbMafName OPONCOKBMAFNAME\n                    [--output_vcf2mafName OUTPUT_VCF2MAFNAME] --input_mappability_bed\n                    INPUT_MAPPABILITY_BED\n                    [--output_mappability_filename OUTPUT_MAPPABILITY_FILENAME]\n                    [--column_name_mappability COLUMN_NAME_MAPPABILITY]\n                    --input_47kchpd_tsv_file INPUT_47KCHPD_TSV_FILE --input_hotspot_tsv_file\n                    INPUT_HOTSPOT_TSV_FILE --input_panmeloid_tsv_file INPUT_PANMELOID_TSV_FILE\n                    [job_order]\n\nchip-var\n\npositional arguments:\n  job_order             Job input json file\n\noptions:\n  -h, --help            show this help message and exit\n  --reference_fasta REFERENCE_FASTA\n  --input_bam_case INPUT_BAM_CASE\n  --bedfile BEDFILE\n  --sample_name SAMPLE_NAME\n  --vardict_allele_frequency_threshold VARDICT_ALLELE_FREQUENCY_THRESHOLD\n  --retain_info RETAIN_INFO\n  --concat_output_name CONCAT_OUTPUT_NAME\n  --vardict_output_vcf_name VARDICT_OUTPUT_VCF_NAME\n  --input_cosmicprevalenceDB_vcf INPUT_COSMICPREVALENCEDB_VCF\n  --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF\n  --snpsift_prevalOpName SNPSIFT_PREVALOPNAME\n  --snpsift_countOpName SNPSIFT_COUNTOPNAME\n  --input_complexity_bed INPUT_COMPLEXITY_BED\n  --output_complexity_filename OUTPUT_COMPLEXITY_FILENAME\n  --column_name_complexity COLUMN_NAME_COMPLEXITY\n  --oncoKbApiToken ONCOKBAPITOKEN\n  --opOncoKbMafName OPONCOKBMAFNAME\n  --output_vcf2mafName OUTPUT_VCF2MAFNAME\n  --input_mappability_bed INPUT_MAPPABILITY_BED\n  --output_mappability_filename OUTPUT_MAPPABILITY_FILENAME\n  --column_name_mappability COLUMN_NAME_MAPPABILITY\n  --input_47kchpd_tsv_file INPUT_47KCHPD_TSV_FILE\n  --input_hotspot_tsv_file INPUT_HOTSPOT_TSV_FILE\n  --input_panmeloid_tsv_file INPUT_PANMELOID_TSV_FILE\n\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmsk-access%2Fchip-var","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmsk-access%2Fchip-var","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmsk-access%2Fchip-var/lists"}