{ "_id": "6a192b5dacfb0bcc41dcdf01", "Package": "gwasvcf", "Title": "Tools for Dealing with GWAS Summary Data in VCF Format", "Version": "0.1.6", "Authors@R": "c(\nperson(\"Gibran\", \"Hemani\", , \"g.hemani@bristol.ac.uk\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0920-1055\")),\nperson(\"Tom\", \"Palmer\", , \"tom.palmer@bristol.ac.uk\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-4655-4511\")),\nperson(\"Rita\", \"Rasteiro\", , \"rita.rasteiro@bristol.ac.uk\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-4217-3060\"))\n)", "Description": "Tools for dealing with GWAS summary data in VCF format.\nIncludes reading, querying, writing, as well as helper\nfunctions such as LD proxy searches.", "License": "MIT + file LICENSE", "URL": "https://github.com/mrcieu/gwasvcf,\nhttps://mrcieu.github.io/gwasvcf/", "BugReports": "https://github.com/mrcieu/gwasvcf/issues", "VignetteBuilder": "knitr", "Remotes": [ "github::mrcieu/genetics.binaRies", "github::mrcieu/gwasglue2" ], "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "SystemRequirements": "GNU unzip, sqlite3", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libsqlite3-dev xz-utils zlib1g-dev", "Repository": "https://mrcieu.r-universe.dev", "Date/Publication": "2026-03-16 10:25:32 UTC", "RemoteUrl": "https://github.com/MRCIEU/gwasvcf", "RemoteRef": "HEAD", "RemoteSha": "53daf45a1e6decb255794877fd50a80c25618fce", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 14:52:04 UTC", "User": "root" }, "Author": "Gibran Hemani [aut, cre] (ORCID:\n),\nTom Palmer [ctb] (ORCID: ),\nRita Rasteiro [ctb] (ORCID: )", "Maintainer": "Gibran Hemani ", "MD5sum": "0c2d056bf9695926e220fb7d73660fcb", "_user": "mrcieu", "_type": "src", "_file": "gwasvcf_0.1.6.tar.gz", "_fileid": "d3f6cd19eddd1db5cebc28d93f7988b7d8d6efbea0dfc0e9dc38279078b1e06e", "_filesize": 725714, "_sha256": "d3f6cd19eddd1db5cebc28d93f7988b7d8d6efbea0dfc0e9dc38279078b1e06e", "_created": "2026-05-28T14:52:04.000Z", "_published": "2026-05-29T05:59:57.761Z", "_distro": "noble", "_jobs": [ { "job": 78445880880, "time": 375, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7269353136" }, { "job": 78445880968, "time": 367, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7269344165" }, { "job": 78445880701, "time": 265, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7270065227" }, { "job": 78445880526, "time": 274, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7284115296" }, { "job": 78445880416, "time": 277, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7269158649" }, { "job": 78445880958, "time": 143, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7269251302" }, { "job": 78445880910, "time": 332, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7269337420" }, { "job": 78445880768, "time": 286, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7269309896" }, { "job": 78445880749, "time": 382, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7269358868" } ], "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26581897490", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/MRCIEU/gwasvcf", "_commit": { "id": "53daf45a1e6decb255794877fd50a80c25618fce", "author": "Tom Palmer ", "committer": "GitHub ", "message": "Merge pull request #43 from ywge03/master\n\nAdd fallback for proxy VCF construction failures on small/single-sample objects", "time": 1773656732 }, "_maintainer": { "name": "Gibran Hemani", "email": "g.hemani@bristol.ac.uk", "login": "explodecomputer", "description": "", "uuid": 1924940, "orcid": "0000-0003-0920-1055" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "genetics.binaRies", "role": "Imports" }, { "package": "GenomeInfoDb", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "gwasglue2", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "RCurl", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "RSQLite", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "VariantAnnotation", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "mrcieu", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-23", "n": 5 }, { "week": "2025-47", "n": 1 }, { "week": "2026-12", "n": 1 } ], "_tags": [ { "name": "v0.1.3", "date": "2025-06-05" }, { "name": "v0.1.4", "date": "2025-06-05" }, { "name": "v0.1.5", "date": "2025-11-21" }, { "name": "v0.1.6", "date": "2026-03-16" } ], "_stars": 105, "_contributors": [ { "user": "remlapmot", "count": 124, "uuid": 3777473 }, { "user": "explodecomputer", "count": 119, "uuid": 1924940 }, { "user": "ritarasteiro", "count": 12, "uuid": 5339671 }, { "user": "marynias", "count": 3, "uuid": 20520409 }, { "user": "ywge03", "count": 3, "uuid": 199273139 }, { "user": "jwr-git", "count": 1, "uuid": 64223802 }, { "user": "mattlee821", "count": 1, "uuid": 30179533 } ], "_userbio": { "uuid": 15654827, "type": "organization", "name": "MRC Integrative Epidemiology Unit" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/gwasvcf" }, "_devurl": "https://github.com/mrcieu/gwasvcf", "_pkgdown": "https://mrcieu.github.io/gwasvcf/", "_searchresults": 166, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gwasvcf.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "%>%", "check_bcftools", "check_plink", "create_ldref_sqlite", "create_pval_index_from_vcf", "create_rsidx_index_from_vcf", "create_rsidx_sub_index", "create_vcf", "get_ld_proxies", "gwasvcf_to_summaryset", "merge_vcf", "parse_chrompos", "proxy_match", "query_chrompos_bcftools", "query_chrompos_file", "query_chrompos_vcf", "query_gwas", "query_pval_bcftools", "query_pval_file", "query_pval_sqlite3", "query_pval_vcf", "query_pvali", "query_rsid_bcftools", "query_rsid_file", "query_rsid_rsidx", "query_rsid_vcf", "query_rsidx", "set_bcftools", "set_plink", "sqlite_ld_proxies", "vcf_to_granges", "vcf_to_tibble", "vcflist_overlaps" ], "_help": [ { "page": "check_bcftools", "title": "Check if the tools_bcftools option is set", "topics": [ "check_bcftools" ] }, { "page": "check_plink", "title": "Check if the tools_plink option is set", "topics": [ "check_plink" ] }, { "page": "create_ldref_sqlite", "title": "Create LD reference sqlite database for tags", "topics": [ "create_ldref_sqlite" ] }, { "page": "create_pval_index_from_vcf", "title": "Create pval index from GWAS-VCF file", "topics": [ "create_pval_index_from_vcf" ] }, { "page": "create_rsidx_index_from_vcf", "title": "Create RSID index from VCF", "topics": [ "create_rsidx_index_from_vcf" ] }, { "page": "create_rsidx_sub_index", "title": "Create new index from existing index using a subset of rsids", "topics": [ "create_rsidx_sub_index" ] }, { "page": "create_vcf", "title": "Create GWAS vcf", "topics": [ "create_vcf" ] }, { "page": "get_ld_proxies", "title": "Find LD proxies for a set of SNPs", "topics": [ "get_ld_proxies" ] }, { "page": "gwasvcf_to_summaryset", "title": "Create a SummarySet", "topics": [ "gwasvcf_to_summaryset" ] }, { "page": "merge_vcf", "title": "Merge two GWAS VCF objects", "topics": [ "merge_vcf" ] }, { "page": "parse_chrompos", "title": "Parse chromosome:position", "topics": [ "parse_chrompos" ] }, { "page": "proxy_match", "title": "Extract SNPs from vcf file", "topics": [ "proxy_match" ] }, { "page": "query_chrompos_bcftools", "title": "Query chromosome and position using bcftools", "topics": [ "query_chrompos_bcftools" ] }, { "page": "query_chrompos_file", "title": "Query vcf file, extracting by chromosome and position", "topics": [ "query_chrompos_file" ] }, { "page": "query_chrompos_vcf", "title": "Query chrompos from vcf object", "topics": [ "query_chrompos_vcf" ] }, { "page": "query_gwas", "title": "Query data from vcf file", "topics": [ "query_gwas" ] }, { "page": "query_pval_bcftools", "title": "Query p-value using bcftools", "topics": [ "query_pval_bcftools" ] }, { "page": "query_pval_file", "title": "Query pval from vcf file", "topics": [ "query_pval_file" ] }, { "page": "query_pval_sqlite3", "title": "Query pval from file using pvali index", "topics": [ "query_pval_sqlite3" ] }, { "page": "query_pval_vcf", "title": "Query based on p-value threshold from vcf", "topics": [ "query_pval_vcf" ] }, { "page": "query_pvali", "title": "Query pvali", "topics": [ "query_pvali" ] }, { "page": "query_rsid_bcftools", "title": "Query", "topics": [ "query_rsid_bcftools" ] }, { "page": "query_rsid_file", "title": "Query vcf file, extracting by rsid", "topics": [ "query_rsid_file" ] }, { "page": "query_rsid_rsidx", "title": "Query rsid from file using rsidx index", "topics": [ "query_rsid_rsidx" ] }, { "page": "query_rsid_vcf", "title": "Query rsid from vcf object", "topics": [ "query_rsid_vcf" ] }, { "page": "query_rsidx", "title": "Query rsidx", "topics": [ "query_rsidx" ] }, { "page": "set_bcftools", "title": "Set bcftools binary location", "topics": [ "set_bcftools" ] }, { "page": "set_plink", "title": "Set plink binary location", "topics": [ "set_plink" ] }, { "page": "sqlite_ld_proxies", "title": "Lookup LD proxies from sqlite database", "topics": [ "sqlite_ld_proxies" ] }, { "page": "VariantAnnotation", "title": "VariantAnnotation", "topics": [ "VariantAnnotation" ] }, { "page": "vcf_to_granges", "title": "Convert vcf format to granges format", "topics": [ "vcf_to_granges" ] }, { "page": "vcf_to_tibble", "title": "Convert vcf format to tibble (data frame)", "topics": [ "vcf_to_tibble" ] }, { "page": "vcflist_overlaps", "title": "Reduce list of VCFs to intersecting regions", "topics": [ "vcflist_overlaps" ] } ], "_readme": "https://github.com/MRCIEU/gwasvcf/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "dplyr", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "genetics.binaRies", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "gwasglue2", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyselect", "UCSC.utils", "utf8", "VariantAnnotation", "vctrs", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "guide.Rmd", "filename": "guide.html", "title": "Reading, querying and writing GWAS summary data in VCF format", "engine": "knitr::rmarkdown", "headings": [ "External tools", "Reading in everything", "Converting to simple dataframes", "Reading in with filters", "Indexing rsid values", "Indexing p-values", "A note about chrompos", "LD proxies", "Using an LD reference panel", "Compiling a list of tagging variants", "Creating the VCF object from a data frame", "Creating a gwasglue2 SummarySet object from a vcf file" ], "created": "2019-11-06 11:13:53", "modified": "2025-06-06 10:24:37", "commits": 11 } ], "_score": 7.1955398965493185, "_indexed": true, "_nocasepkg": "gwasvcf", "_universes": [ "mrcieu", "explodecomputer" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.6", "date": "2026-05-28T14:56:48.000Z", "distro": "noble", "commit": "53daf45a1e6decb255794877fd50a80c25618fce", "fileid": "25ca9209facf978d20d8ee920f35578da5d5b49e1c5027f7f194711202b833aa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26581897490" }, { "r": "4.6.0", "os": "linux", "version": "0.1.6", "date": "2026-05-28T14:56:37.000Z", "distro": "noble", "commit": "53daf45a1e6decb255794877fd50a80c25618fce", "fileid": "91d18d8660ecf142e7b787fb28252cb2ebb8519410fbeddf5c65b0dab19707f5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26581897490" }, { "r": "4.5.3", "os": "mac", "version": "0.1.6", "date": "2026-05-28T15:26:04.000Z", "commit": "53daf45a1e6decb255794877fd50a80c25618fce", "fileid": "96f80f0706a1b9a513b4027eb59a17a2bae7f1f19619bb82bdbfe6d8849fc2d6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26581897490" }, { "r": "4.6.0", "os": "mac", "version": "0.1.6", "date": "2026-05-29T05:56:49.000Z", "commit": "53daf45a1e6decb255794877fd50a80c25618fce", "fileid": "715b77da9fcfa58d64d9095db4c77cc0bebb64b56dcc0b09bab1d6e7161dcd30", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26581897490" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.6", "date": "2026-05-28T14:56:22.000Z", "commit": "53daf45a1e6decb255794877fd50a80c25618fce", "fileid": "25cbde07d766c48737f96f4dc680c427028ea24a1e2313a4ada449ae60c0eb04", "status": "success", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26581897490" }, { "r": "4.7.0", "os": "win", "version": "0.1.6", "date": "2026-05-28T14:56:13.000Z", "commit": "53daf45a1e6decb255794877fd50a80c25618fce", "fileid": "8c322da1a41adeec3f5734344b255fd6389d73a4e31ad3c4fe9edf0c76e2cdfd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26581897490" }, { "r": "4.5.3", "os": "win", "version": "0.1.6", "date": "2026-05-28T14:55:14.000Z", "commit": "53daf45a1e6decb255794877fd50a80c25618fce", "fileid": "a54d2fdba9916f886ce087b6e8e0722749fc00c15ac4e1d4ff7d4ecc3d66d22c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26581897490" }, { "r": "4.6.0", "os": "win", "version": "0.1.6", "date": "2026-05-28T14:57:09.000Z", "commit": "53daf45a1e6decb255794877fd50a80c25618fce", "fileid": "22c59331d01ca609b2d3df5823ac1561e3a75a555a46cba182f8610e485b768b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/26581897490" } ] }