{
  "_id": "6a60a457c766cc6deb6aa14e",
  "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"
  ],
  "Config/roxygen2/markdown": "TRUE",
  "Config/roxygen2/version": "8.0.0",
  "Encoding": "UTF-8",
  "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": "2026-07-22 09:05:31 UTC",
  "RemoteUrl": "https://github.com/MRCIEU/gwasvcf",
  "RemoteRef": "HEAD",
  "RemoteSha": "89154bc50651538a6d7d91494e78c04fcb62bc98",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-22 10:59:00 UTC",
    "User": "root"
  },
  "Author": "Gibran Hemani [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0920-1055>),\nTom Palmer [ctb] (ORCID: <https://orcid.org/0000-0003-4655-4511>),\nRita Rasteiro [ctb] (ORCID: <https://orcid.org/0000-0002-4217-3060>)",
  "Maintainer": "Gibran Hemani <g.hemani@bristol.ac.uk>",
  "_user": "mrcieu",
  "_type": "src",
  "_file": "gwasvcf_0.1.6.tar.gz",
  "_fileid": "https://r2.ropensci.org/076acc81c25a0dd2ef355305d1318bbb77b8dbb78336155236e294093dd64ce0",
  "_filesize": 725549,
  "_sha256": "076acc81c25a0dd2ef355305d1318bbb77b8dbb78336155236e294093dd64ce0",
  "_expires": "2026-10-30T11:07:01.000Z",
  "_created": "2026-07-22T10:59:00.000Z",
  "_published": "2026-07-22T11:07:03.199Z",
  "_jobs": [
    {
      "job": 88903491223,
      "time": 395,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8527249029"
    },
    {
      "job": 88903491273,
      "time": 366,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8527236812"
    },
    {
      "job": 88903491228,
      "time": 251,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8527209421"
    },
    {
      "job": 88903491199,
      "time": 389,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8527256704"
    },
    {
      "job": 88902180024,
      "time": 387,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8527082078"
    },
    {
      "job": 88903491181,
      "time": 157,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8527149814"
    },
    {
      "job": 88903491230,
      "time": 312,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8527215374"
    },
    {
      "job": 88903491224,
      "time": 299,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8527210893"
    },
    {
      "job": 88903491239,
      "time": 286,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8527204522"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/29913607125",
  "_status": "success",
  "_upstream": "https://github.com/MRCIEU/gwasvcf",
  "_commit": {
    "id": "89154bc50651538a6d7d91494e78c04fcb62bc98",
    "author": "Tom Palmer <remlapmot@hotmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #44 from remlapmot/fix-gha\n\nUpdate GitHub Actions check workflow",
    "time": 1784711131
  },
  "_maintainer": {
    "name": "Gibran Hemani",
    "email": "g.hemani@bristol.ac.uk",
    "login": "explodecomputer",
    "description": "",
    "uuid": 1924940,
    "orcid": "0000-0003-0920-1055"
  },
  "_distro": "resolute",
  "_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": "2025-47",
      "n": 1
    },
    {
      "week": "2026-12",
      "n": 1
    },
    {
      "week": "2026-30",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "v0.1.5",
      "date": "2025-11-21"
    },
    {
      "name": "v0.1.6",
      "date": "2026-03-16"
    }
  ],
  "_stars": 110,
  "_contributors": [
    {
      "user": "remlapmot",
      "count": 130,
      "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",
    "followers": 252
  },
  "_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": 160,
  "_rbuild": "4.6.1",
  "_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",
    "LICENSE",
    "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": 7.199755177253475,
  "_indexed": true,
  "_nocasepkg": "gwasvcf",
  "_universes": [
    "mrcieu",
    "explodecomputer"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.6",
      "date": "2026-07-22T11:02:19.000Z",
      "distro": "resolute",
      "commit": "89154bc50651538a6d7d91494e78c04fcb62bc98",
      "fileid": "https://r2.ropensci.org/81705fbab0880e4b020cfd5d8589a96a2d3f91cd6cbfcac29d97f6c279b726cb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/29913607125"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.1.6",
      "date": "2026-07-22T11:02:15.000Z",
      "distro": "resolute",
      "commit": "89154bc50651538a6d7d91494e78c04fcb62bc98",
      "fileid": "https://r2.ropensci.org/d019a4a6c1b3ff56268e6d139d9dd75d8968582071cfea5512dd38b296002017",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/29913607125"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.6",
      "date": "2026-07-22T11:01:49.000Z",
      "commit": "89154bc50651538a6d7d91494e78c04fcb62bc98",
      "fileid": "https://r2.ropensci.org/cf56c6df25657ea7f38a357e4bf4d6d57832fb2fe32e3a22d6f90172fe7cfef0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/29913607125"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.1.6",
      "date": "2026-07-22T11:02:17.000Z",
      "commit": "89154bc50651538a6d7d91494e78c04fcb62bc98",
      "fileid": "https://r2.ropensci.org/98b0101f3585cf85961836151fd00e899bc1a18e0a3c9758c0d522ddac381416",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/29913607125"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.6",
      "date": "2026-07-22T11:02:10.000Z",
      "commit": "89154bc50651538a6d7d91494e78c04fcb62bc98",
      "fileid": "https://r2.ropensci.org/c4b12524602b4f698ba686789ea45ab0e4c217c74d988502173b07bc5b4b7831",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/29913607125"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.6",
      "date": "2026-07-22T11:01:24.000Z",
      "commit": "89154bc50651538a6d7d91494e78c04fcb62bc98",
      "fileid": "https://r2.ropensci.org/5304ffd1c497d9c4e5e682b77cb45e6beea8ef9629395b69af7142ce24eaa58b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/29913607125"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.6",
      "date": "2026-07-22T11:01:15.000Z",
      "commit": "89154bc50651538a6d7d91494e78c04fcb62bc98",
      "fileid": "https://r2.ropensci.org/5d60cfea698cccd693ff4f478ecd0c614f272083fecc31c6a481bad86dd27aaa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/29913607125"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.1.6",
      "date": "2026-07-22T11:00:58.000Z",
      "commit": "89154bc50651538a6d7d91494e78c04fcb62bc98",
      "fileid": "https://r2.ropensci.org/b96286e6aa1776a91dffaf2fca4426651b09bd841f573d8db346d76907cd4fcb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/29913607125"
    }
  ]
}