{"id":13752626,"url":"https://github.com/lh3/dipcall","last_synced_at":"2025-10-25T13:42:14.900Z","repository":{"id":54976385,"uuid":"212490128","full_name":"lh3/dipcall","owner":"lh3","description":"Reference-based variant calling pipeline for a pair of phased haplotype assemblies","archived":false,"fork":false,"pushed_at":"2021-06-06T20:36:10.000Z","size":24,"stargazers_count":100,"open_issues_count":8,"forks_count":10,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-05-07T08:12:17.958Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lh3.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-10-03T03:29:52.000Z","updated_at":"2025-03-13T08:46:08.000Z","dependencies_parsed_at":"2022-08-14T08:00:27.541Z","dependency_job_id":null,"html_url":"https://github.com/lh3/dipcall","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/lh3/dipcall","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fdipcall","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fdipcall/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fdipcall/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fdipcall/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lh3","download_url":"https://codeload.github.com/lh3/dipcall/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fdipcall/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278629799,"owners_count":26018628,"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":"2025-10-06T02:00:05.630Z","response_time":65,"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":[],"created_at":"2024-08-03T09:01:08.491Z","updated_at":"2025-10-06T15:10:17.509Z","avatar_url":"https://github.com/lh3.png","language":"JavaScript","readme":"## Getting Started\n\n```sh\nwget https://github.com/lh3/dipcall/releases/download/v0.3/dipcall-0.3_x64-linux.tar.bz2\ntar -jxf dipcall-0.3_x64-linux.tar.bz2\n# for female\ndipcall.kit/run-dipcall prefix hs38.fa pat.fa.gz mat.fa.gz \u003e prefix.mak\n# or for male, requiring PAR regions in BED\n# dipcall.kit/run-dipcall -x dipcall.kit/hs38.PAR.bed prefix hs38.fa pat.fa.gz mat.fa.gz \u003e prefix.mak\nmake -j2 -f prefix.mak\n```\n\n## Introduction\n\nDipcall is a reference-based variant calling pipeline for a pair of phased\nhaplotype assemblies. It was originally developed for constructing the\n[syndip][syndip] benchmark dataset and has been applied to other phased\nassemblies, too. Dipcall can call small variants and long INDELs as long as\nthey are contained in minimap2 alignment.\n\nIf you use dipcall, please cite\n\n\u003e Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D\n\u003e (2018) A synthetic-diploid benchmark for accurate variant-calling evaluation.\n\u003e Nat Methods, 15:595-597. [PMID:30013044]\n\n## Output\n\nThe final output of dipcall includes two files: *prefix*.dip.vcf.gz and\n*prefix*.dip.bed. A raw variant call is made in the VCF if a non-reference\nallele is observed in any alignments \u003e=50kb and mapped with mapping quality \u003e=5.\nIn the VCF, dipcall sets a `HET1` filter if parent1 is a heterozygous at the\nraw variant; dipcall sets a `GAP1` filter if no \u003e=50kb alignment from parent1\ncovers the variant. Note that if a call is covered by multiple \u003e=50kb\nalignments in the same parent but the alignments all have the same allele, the\ncall is not filtered in the VCF.\n\nThe BED file gives the confident regions. A base is included in the BED if 1)\nit is covered by one \u003e=50kb alignment with mapQ\u003e=5 from each parent and 2)\nit is not covered by other \u003e=10kb alignments in each parent. Nearly all calls\nfiltered in the VCF are excluded in the BED, except very rare edge cases.\nHowever, a fraction of unfiltered calls in the VCF may also be excluded by the\nBED. The BED file applies more stringent filter.\n\nThe above is applied to autosomes and female chrX. For a male sample, parent1\nis assumed to be the father and parent2 the mother. Dipcall treats PARs the\nsame way as autosomes. However, outside PARs, dipcall filters out chrX regions\ncovered by father contigs and filters out chrY regions covered by mother\ncontigs. To make proper calls on sex chromosomes, users should hard mask PARs\non the reference chrY.\n\n[syndip]: https://github.com/lh3/CHM-eval\n","funding_links":[],"categories":["Ranked by starred repositories"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flh3%2Fdipcall","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flh3%2Fdipcall","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flh3%2Fdipcall/lists"}