{"id":21318839,"url":"https://github.com/sydney-informatics-hub/slivar_vcffiltering","last_synced_at":"2026-07-17T06:33:26.653Z","repository":{"id":107913377,"uuid":"491379100","full_name":"Sydney-Informatics-Hub/Slivar_VCFfiltering","owner":"Sydney-Informatics-Hub","description":"Running Slivar CLI tool to query and filter group/trio VCF files","archived":false,"fork":false,"pushed_at":"2022-05-12T06:53:49.000Z","size":7,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-10-24T06:05:23.972Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","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/Sydney-Informatics-Hub.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-05-12T05:41:30.000Z","updated_at":"2022-10-27T08:09:07.000Z","dependencies_parsed_at":null,"dependency_job_id":"4db42091-e183-4cd1-8a4b-1d166029a9fc","html_url":"https://github.com/Sydney-Informatics-Hub/Slivar_VCFfiltering","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Sydney-Informatics-Hub/Slivar_VCFfiltering","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FSlivar_VCFfiltering","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FSlivar_VCFfiltering/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FSlivar_VCFfiltering/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FSlivar_VCFfiltering/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Sydney-Informatics-Hub","download_url":"https://codeload.github.com/Sydney-Informatics-Hub/Slivar_VCFfiltering/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Sydney-Informatics-Hub%2FSlivar_VCFfiltering/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35571460,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-17T02:00:06.162Z","response_time":116,"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":"2024-11-21T19:24:11.313Z","updated_at":"2026-07-17T06:33:26.648Z","avatar_url":"https://github.com/Sydney-Informatics-Hub.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Slivar_VCFfiltering\nRunning Slivar CLI tool to query and filter group/trio VCF files\n\n## Overview\n\nPerform filtering of WGS trios to identify candidate gene variants. In the script provided as an example, SNVs and indels were filtered for coding variants in affected individuals that followed autosomal recessive, de novo and compound heterozygous inheritance patterns.     \n\n### Software and versions \nbcftools/1.14   \nslivar/0.2.7     \n\n## Input files \n\n**HG38 Reference materials**   \nHomo_sapiens_assembly38.fasta  \nHomo_sapiens.GRCh38.105.gff3.gz # from Ensembl ftp site \n\n**VCF**   \nJoint called VCF file for cohort was created using GATK. The VCF had to be decomposed before running Slivar. Variant sites were annotated with bcftools csq and Ensembl's GFF3 file for Hg38. Commands for both of these steps are included in the script. \n\n**pedigree**  \n\n```\n#FID  IID PID MID SEX PHENO\ntrio1   sample1 sample2  sample3  0       2\ntrio1   sample2  0       0       1       1\ntrio1   sample3  0       0       2       1\ntrio2   sample4 sample5  sample6  1       2\ntrio2   sample5  0       0       1       1\ntrio2   sample6  0       0       2       1\n```\n\n**slivar-functions.js**  \nRequired by Slivar to define different expressions for filtering. Downloaded from [here](https://github.com/brentp/slivar/blob/master/js/slivar-functions.js)\n\n## Running the script \n\nOn Usyd Artemis HPC, run as:  \n\n`qsub run_slivar.sh`  \n\nThis script annotated the cohort VCF using the GFF3 file, and prepared it for Slivar and output two filtered VCF files. One containing all rare impactful variants that matched de novo, recessive, and comphet expressions in each trio. The other VCF contained trans compound het variants.  \n\nReformatted Slivar .vcfs to .tsv using `tsv_slivar.sh`. On USyd Artemis HPC, run as: `bash tsv_slivar.sh`   \n\n## Resources \n[Slivar github repository and documentation](https://github.com/brentp/slivar)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsydney-informatics-hub%2Fslivar_vcffiltering","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsydney-informatics-hub%2Fslivar_vcffiltering","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsydney-informatics-hub%2Fslivar_vcffiltering/lists"}