{"id":13296977,"url":"https://github.com/kids-first/kf-genotype-refinement-workflow","last_synced_at":"2026-03-01T11:37:05.922Z","repository":{"id":89645903,"uuid":"140012723","full_name":"kids-first/kf-genotype-refinement-workflow","owner":"kids-first","description":null,"archived":false,"fork":false,"pushed_at":"2019-11-19T21:01:34.000Z","size":302,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":8,"default_branch":"master","last_synced_at":"2023-02-28T03:23:09.668Z","etag":null,"topics":["bioinformatics","cwl"],"latest_commit_sha":null,"homepage":null,"language":"Common Workflow Language","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kids-first.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2018-07-06T17:23:14.000Z","updated_at":"2020-05-27T08:46:37.000Z","dependencies_parsed_at":null,"dependency_job_id":"6d7340e6-324f-4684-beca-4f6c2fb87142","html_url":"https://github.com/kids-first/kf-genotype-refinement-workflow","commit_stats":null,"previous_names":[],"tags_count":0,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kids-first%2Fkf-genotype-refinement-workflow","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kids-first%2Fkf-genotype-refinement-workflow/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kids-first%2Fkf-genotype-refinement-workflow/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kids-first%2Fkf-genotype-refinement-workflow/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kids-first","download_url":"https://codeload.github.com/kids-first/kf-genotype-refinement-workflow/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":242823770,"owners_count":20191057,"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","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","cwl"],"created_at":"2024-07-29T17:21:20.694Z","updated_at":"2026-03-01T11:37:05.881Z","avatar_url":"https://github.com/kids-first.png","language":"Common Workflow Language","funding_links":[],"categories":[],"sub_categories":[],"readme":"# kfdrc genotype refinement workflow\n\n## Implementation of Broad Institute Genotype Refinement Workflow\n\u003ca href=\"https://software.broadinstitute.org/gatk/documentation/article?id=11074\"\u003e Genotype Refinement workflow for germline short variants\u003c/a\u003e\n+ Note, step 4 is skipped\n+ variant effect predictor run at the end to annotate vcf and get variant summary stats\n\n## basic info\n- tool images: https://hub.docker.com/r/kfdrc/\n- dockerfiles: https://github.com/d3b-center/bixtools\n- tested with\n  - rabix-v1.0.5: https://github.com/rabix/bunny/releases/tag/v1.0.5\n\n## inputs:\n\n+ Uses output gvcf from https://github.com/kids-first/kf-jointgenotyping-workflow\n\n```yaml\nped:\n  class: File\n  path: FM_XXXXXX.ped\nreference:\n  class: File\n  path: Homo_sapiens_assembly38.fasta\ncache: File\n  class: File\n  path: homo_sapiens_vep_93_GRCh38_convert_cache.tar.gz # tar gzipped vep93 cache file\nsnp_sites:\n  class: File\n  path: 1000G_phase3_v4_20130502.sites.hg38.vcf\nvqsr_vcf:\n  class: File\n  path: vqsr_vcf.vcf.gz # A recalibrated variants gvcf from VQSR\noutput_basename: vqsr_vcf\n```\n![Alt text](./genotype-refinement-workflow.png?raw=true \"Workflow diagram\")\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkids-first%2Fkf-genotype-refinement-workflow","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkids-first%2Fkf-genotype-refinement-workflow","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkids-first%2Fkf-genotype-refinement-workflow/lists"}