{"id":28395207,"url":"https://github.com/databiosphere/xvcfview","last_synced_at":"2025-06-27T01:31:17.679Z","repository":{"id":42461473,"uuid":"386054234","full_name":"DataBiosphere/xvcfview","owner":"DataBiosphere","description":"A WDL workflow to subset, subsample, and filter VCF files using bcftools.","archived":false,"fork":false,"pushed_at":"2022-04-04T23:59:44.000Z","size":411,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-06-01T06:52:29.127Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"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/DataBiosphere.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}},"created_at":"2021-07-14T19:27:56.000Z","updated_at":"2021-11-30T19:12:08.000Z","dependencies_parsed_at":"2022-09-13T17:00:59.264Z","dependency_job_id":null,"html_url":"https://github.com/DataBiosphere/xvcfview","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/DataBiosphere/xvcfview","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataBiosphere%2Fxvcfview","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataBiosphere%2Fxvcfview/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataBiosphere%2Fxvcfview/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataBiosphere%2Fxvcfview/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DataBiosphere","download_url":"https://codeload.github.com/DataBiosphere/xvcfview/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataBiosphere%2Fxvcfview/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262172367,"owners_count":23269993,"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":[],"created_at":"2025-05-31T19:39:30.008Z","updated_at":"2025-06-27T01:31:17.663Z","avatar_url":"https://github.com/DataBiosphere.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# xvcfview\n\nThis workflow provides the full power of [bcftools view](http://samtools.github.io/bcftools/bcftools.html#view) to subset, subsample, and filter VCF files.\n\n## input\n\nAll input files are referenced with either gs:// or drs:// URIs.\n\n\n| parameter | required | default | description |\n| --------- | -------- | :---------: | ----------- |\n| `input_vcf` | required | | Input VCF file. |\n| `input_vcf_index` | optional | | VCF index file. If omitted, an index is created during execution. Instructions for creating index files are [here](http://samtools.github.io/bcftools/bcftools.html#index). |\n| `samples` | optional | | File of samples to be included in the output VCF. There should one sample per line. Additional information is [here](http://samtools.github.io/bcftools/bcftools.html#common_options). |\n| `regions` | optional | | File of regions to be included in the output VCF. The file should contain tab separated columns of chromosome (e.g. 'chr15'), start position, and optionally end position. Additional information is [here](http://samtools.github.io/bcftools/bcftools.html#common_options). |\n| `view_options` | optional | `-Oz` | Additional parameters to pass to the [bcftools view](http://samtools.github.io/bcftools/bcftools.html#view) command. If modified, `view_options` should typically include `-Oz` to produce a gzipped output VCF. |\n| `filters` | optional | | Filter arguments to pass into [bcftools view](http://samtools.github.io/bcftools/bcftools.html#view). Filters will be applied in a separate, subsequent, call to `bcftools view`. |\n| `output_filename` | optional | `output.vcf.gz` | Name of the output vcf file. |\n| `cpu` | optional | `8` | Number of CPU cores. |\n| `memory` | optional | `64` | Amount of RAM in GB |\n| `preemptible` | optional | `0` | Whether to use preemptible instances, which are cheaper but my be revoked during execution. |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabiosphere%2Fxvcfview","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatabiosphere%2Fxvcfview","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatabiosphere%2Fxvcfview/lists"}