{"id":20386928,"url":"https://github.com/cmdcolin/vcfverifier","last_synced_at":"2025-04-12T09:54:28.148Z","repository":{"id":50541155,"uuid":"519376189","full_name":"cmdcolin/vcfverifier","owner":"cmdcolin","description":"Check that a VCF matches a given reference genome","archived":false,"fork":false,"pushed_at":"2024-12-04T16:52:36.000Z","size":46,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-12T09:54:18.105Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Rust","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/cmdcolin.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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":"2022-07-29T23:50:35.000Z","updated_at":"2025-03-21T16:16:50.000Z","dependencies_parsed_at":"2024-11-15T02:41:44.481Z","dependency_job_id":"848e04bb-24d8-45e1-a240-9709c281e0b8","html_url":"https://github.com/cmdcolin/vcfverifier","commit_stats":{"total_commits":11,"total_committers":1,"mean_commits":11.0,"dds":0.0,"last_synced_commit":"39da8b88ae4bb6a0456723549657980d9fdb615b"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fvcfverifier","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fvcfverifier/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fvcfverifier/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmdcolin%2Fvcfverifier/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmdcolin","download_url":"https://codeload.github.com/cmdcolin/vcfverifier/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248550634,"owners_count":21122932,"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":"2024-11-15T02:41:38.849Z","updated_at":"2025-04-12T09:54:28.113Z","avatar_url":"https://github.com/cmdcolin.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"# vcfverifier\n\nChecks that a given VCF file matches a given assembly in FASTA format by\nchecking that the REF column matches the FASTA file for each record in the\nFASTA file (case insensitive)\n\n## Install\n\nFirst install rust, probably with rustup https://rustup.rs/\n\nThen\n\n```\ncargo install vcfverifier\n```\n\n## Usage\n\n```\n## Generated FASTA index (fai)\nsamtools faidx myfile.fa\n\n## Run the verifier\nvcfverifier --fasta myfile.fa --vcf myfile.vcf.gz\n```\n\nAllows plaintext, gzip, or bgzip vcf files as input to the --vcf flag\n\n## Approx speed\n\nProcessing chr1 (6.5M rows) of the 1000 genomes dataset takes ~24seconds\n\n```\n$ time vcfverifier --fasta hs37d5.fa --vcf ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz\nLines processed: 6468347\nNo mismatching lines found\nvcfverifier --fasta ~/Downloads/hs37d5.fa --vcf   24.07s user 0.26s system 99% cpu 24.330 total\n\n```\n\n## Note\n\nMy first rust project!\n\nUses faimm to memory-map the indexed FASTA file, keeping memory usage low (the\nentire FASTA does not have to be loaded into memory and the VCF is read line by\nline) https://github.com/veldsla/faimm\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fvcfverifier","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdcolin%2Fvcfverifier","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fvcfverifier/lists"}