{
  "_id": "6a23d193530b9bc726be3197",
  "Package": "varitas",
  "Type": "Package",
  "Title": "Variant Calling in Targeted Analysis Sequencing Data",
  "Version": "0.0.2",
  "Date": "2020-11-03",
  "Authors@R": "c(\nperson(\"Adam\", \"Mills\", role = c(\"aut\", \"cre\"), email = \"Adam.Mills@icr.ac.uk\"),\nperson(\"Erle\", \"Holgersen\", role = \"aut\"),\nperson(\"Ros\", \"Cutts\", role = \"aut\"),\nperson(\"Syed\", \"Haider\", role = \"aut\", email = \"Syed.Haider@icr.ac.uk\")\n)",
  "Description": "Multi-caller variant analysis pipeline for targeted\nanalysis sequencing (TAS) data. Features a modular, automated\nworkflow that can start with raw reads and produces a\nuser-friendly PDF summary and a spreadsheet containing\nconsensus variant information.",
  "SystemRequirements": "perl, bedtools (>=2.27.1), bwa",
  "License": "GPL-2",
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  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-06 07:48:49 UTC",
    "User": "root"
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  "Author": "Adam Mills [aut, cre], Erle Holgersen [aut], Ros Cutts [aut],\nSyed Haider [aut]",
  "Maintainer": "Adam Mills <Adam.Mills@icr.ac.uk>",
  "Config/pak/sysreqs": "perl",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2020-11-13 23:30:03 UTC",
  "RemoteUrl": "https://github.com/cran/varitas",
  "RemoteRef": "HEAD",
  "RemoteSha": "603e4ec1d6d90678eb54486f7a0faf6a76a14114",
  "MD5sum": "eeeed8e806660c7217e90e49b784f9ee",
  "_user": "cran",
  "_type": "src",
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  "_created": "2026-06-06T07:48:49.000Z",
  "_published": "2026-06-06T07:51:47.775Z",
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    "author": "Adam Mills <Adam.Mills@icr.ac.uk>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.0.2\n",
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      "package": "stringr",
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    "get.varitas.options",
    "overwrite.varitas.options",
    "prepare.miniseq.specifications",
    "read.yaml",
    "run.alignment",
    "run.annotation",
    "run.post.processing",
    "run.variant.calling",
    "run.varitas.pipeline",
    "run.varitas.pipeline.hybrid",
    "set.varitas.options"
  ],
  "_help": [
    {
      "page": "add.option",
      "title": "add.option",
      "topics": [
        "add.option"
      ]
    },
    {
      "page": "alternate.gene.sort",
      "title": "alternate.gene.sort",
      "topics": [
        "alternate.gene.sort"
      ]
    },
    {
      "page": "build.variant.specification",
      "title": "build.variant.specification",
      "topics": [
        "build.variant.specification"
      ]
    },
    {
      "page": "caller.overlap.venn.diagram",
      "title": ". Make Venn diagram of variant caller overlap",
      "topics": [
        "caller.overlap.venn.diagram"
      ]
    },
    {
      "page": "capitalize.caller",
      "title": "capitalize.caller",
      "topics": [
        "capitalise.caller",
        "capitalize.caller"
      ]
    },
    {
      "page": "classify.variant",
      "title": "classify.variant",
      "topics": [
        "classify.variant"
      ]
    },
    {
      "page": "convert.ides.output",
      "title": "Convert output of iDES step 1 to variant call format",
      "topics": [
        "convert.ides.output"
      ]
    },
    {
      "page": "create.directories",
      "title": "create.directories",
      "topics": [
        "create.directories"
      ]
    },
    {
      "page": "date.stamp.file.name",
      "title": "date.stamp.file.name",
      "topics": [
        "date.stamp.file.name",
        "datestamp.file.name",
        "datestamp.filename"
      ]
    },
    {
      "page": "extract.sample.ids",
      "title": "Extract sample IDs from file paths",
      "topics": [
        "extract.sample.ids"
      ]
    },
    {
      "page": "filter.variant.file",
      "title": "Filter variants in file.",
      "topics": [
        "filter.variant.file"
      ]
    },
    {
      "page": "filter.variants",
      "title": "Filter variant calls",
      "topics": [
        "filter.variants"
      ]
    },
    {
      "page": "fix.lofreq.af",
      "title": "fix.lofreq.af",
      "topics": [
        "fix.lofreq.af"
      ]
    },
    {
      "page": "fix.names",
      "title": "Fix variant call column names",
      "topics": [
        "fix.names"
      ]
    },
    {
      "page": "fix.varscan.af",
      "title": "fix.varscan.af",
      "topics": [
        "fix.varscan.af"
      ]
    },
    {
      "page": "get.base.substitution",
      "title": "Get base substitution",
      "topics": [
        "get.base.substitution"
      ]
    },
    {
      "page": "get.bed.chromosomes",
      "title": "get.bed.chromosomes",
      "topics": [
        "get.bed.chromosomes"
      ]
    },
    {
      "page": "get.buildver",
      "title": "get.buildver",
      "topics": [
        "get.buildver"
      ]
    },
    {
      "page": "get.colours",
      "title": "Generate a colour scheme",
      "topics": [
        "get.colours"
      ]
    },
    {
      "page": "get.coverage.by.amplicon",
      "title": "Process sample coverage per amplicon data",
      "topics": [
        "get.coverage.by.amplicon"
      ]
    },
    {
      "page": "get.coverage.by.sample.statistics",
      "title": "Get statistics about coverage per sample",
      "topics": [
        "get.coverage.by.sample.statistics"
      ]
    },
    {
      "page": "get.fasta.chromosomes",
      "title": "get.fasta.chromosomes",
      "topics": [
        "get.fasta.chromosomes"
      ]
    },
    {
      "page": "get.file.path",
      "title": "get.file.path",
      "topics": [
        "get.file.path"
      ]
    },
    {
      "page": "get.filters",
      "title": "get.filters",
      "topics": [
        "get.filters"
      ]
    },
    {
      "page": "get.gene",
      "title": "get.gene",
      "topics": [
        "get.gene"
      ]
    },
    {
      "page": "get.miniseq.sample.files",
      "title": "get.miniseq.sample.files",
      "topics": [
        "get.miniseq.sample.files"
      ]
    },
    {
      "page": "get.option",
      "title": "Helper function to recursively get an VariTAS option",
      "topics": [
        "get.option"
      ]
    },
    {
      "page": "get.panel.coverage.by.gene",
      "title": "Summarise panel coverage by gene",
      "topics": [
        "get.panel.coverage.by.gene"
      ]
    },
    {
      "page": "get.pool.from.panel.data",
      "title": "Get pool corresponding to each amplicon",
      "topics": [
        "get.pool.from.panel.data"
      ]
    },
    {
      "page": "get.varitas.options",
      "title": "Return VariTAS settings",
      "topics": [
        "get.varitas.options"
      ]
    },
    {
      "page": "get.vcf.chromosomes",
      "title": "get.vcf.chromosomes",
      "topics": [
        "get.vcf.chromosomes"
      ]
    },
    {
      "page": "in.varitas.options",
      "title": "Check if a key is in VariTAS options",
      "topics": [
        "in.varitas.options"
      ]
    },
    {
      "page": "logical.to.character",
      "title": "logical.to.character",
      "topics": [
        "logical.to.character"
      ]
    },
    {
      "page": "make.command.line.call",
      "title": "Make string with command line call from its individual components",
      "topics": [
        "make.command.line.call"
      ]
    },
    {
      "page": "mean.field.value",
      "title": "mean.field.value",
      "topics": [
        "mean.field.value"
      ]
    },
    {
      "page": "merge.ides.annotation",
      "title": "Merge potential iDES calls with variant annotation.",
      "topics": [
        "merge.ides.annotation"
      ]
    },
    {
      "page": "merge.variants",
      "title": "Merge variants",
      "topics": [
        "merge.variants"
      ]
    },
    {
      "page": "overwrite.varitas.options",
      "title": "overwrite.varitas.options",
      "topics": [
        "overwrite.varitas.options"
      ]
    },
    {
      "page": "parse.job.dependencies",
      "title": "Parse job dependencies",
      "topics": [
        "parse.job.dependencies"
      ]
    },
    {
      "page": "plot.amplicon.coverage.per.sample",
      "title": "plot.amplicon.coverage.per.sample",
      "topics": [
        "plot.amplicon.coverage.per.sample"
      ]
    },
    {
      "page": "plot.coverage.by.genome.order",
      "title": "Plot amplicon coverage by genome order",
      "topics": [
        "plot.coverage.by.genome.order"
      ]
    },
    {
      "page": "plot.coverage.by.sample",
      "title": "plot.coverage.by.sample",
      "topics": [
        "plot.coverage.by.sample"
      ]
    },
    {
      "page": "plot.ontarget.percent",
      "title": "plot.ontarget.percent",
      "topics": [
        "plot.ontarget.percent"
      ]
    },
    {
      "page": "plot.paired.percent",
      "title": "plot.paired.percent",
      "topics": [
        "plot.paired.percent"
      ]
    },
    {
      "page": "post.processing",
      "title": "Post-processing of variants to generate outputs",
      "topics": [
        "post.processing"
      ]
    },
    {
      "page": "prepare.bam.specification",
      "title": "Prepare BAM specification data frame to standardized format for downstream analyses.",
      "topics": [
        "prepare.bam.specification"
      ]
    },
    {
      "page": "prepare.fastq.specification",
      "title": "prepare.fastq.specification",
      "topics": [
        "prepare.fastq.specification"
      ]
    },
    {
      "page": "prepare.miniseq.specifications",
      "title": "prepare.miniseq.specifications",
      "topics": [
        "prepare.miniseq.specifications"
      ]
    },
    {
      "page": "prepare.vcf.specification",
      "title": "prepare.vcf.specification",
      "topics": [
        "prepare.vcf.specification"
      ]
    },
    {
      "page": "process.coverage.reports",
      "title": "Process coverageBed reports",
      "topics": [
        "process.coverage.reports"
      ]
    },
    {
      "page": "process.sample.contamination.checks",
      "title": "Process sample contamination checks",
      "topics": [
        "process.sample.contamination.checks"
      ]
    },
    {
      "page": "process.total.coverage.statistics",
      "title": "Process total coverage statistics",
      "topics": [
        "process.total.coverage.statistics"
      ]
    },
    {
      "page": "read.all.calls",
      "title": "read.all.calls",
      "topics": [
        "read.all.calls"
      ]
    },
    {
      "page": "read.ides.file",
      "title": "Read iDES output",
      "topics": [
        "read.ides.file"
      ]
    },
    {
      "page": "read.variant.calls",
      "title": "Read variant calls from file and format for ease of downstream analyses.",
      "topics": [
        "read.variant.calls"
      ]
    },
    {
      "page": "read.yaml",
      "title": "read.yaml",
      "topics": [
        "read.yaml"
      ]
    },
    {
      "page": "run.alignment",
      "title": "Run alignment",
      "topics": [
        "run.alignment"
      ]
    },
    {
      "page": "run.alignment.sample",
      "title": "Run alignment for a single sample",
      "topics": [
        "run.alignment.sample"
      ]
    },
    {
      "page": "run.all.scripts",
      "title": "Run all the generated bash scripts without HPC commands",
      "topics": [
        "run.all.scripts"
      ]
    },
    {
      "page": "run.annotation",
      "title": "Run annotation on a set of VCF files",
      "topics": [
        "run.annotation"
      ]
    },
    {
      "page": "run.annovar.vcf",
      "title": "Run ANNOVAR on a VCF file",
      "topics": [
        "run.annovar.vcf"
      ]
    },
    {
      "page": "run.filtering.txt",
      "title": "Run filtering on an ANNOVAR-annotated txt file",
      "topics": [
        "run.filtering.txt"
      ]
    },
    {
      "page": "run.ides",
      "title": "Run iDES",
      "topics": [
        "run.ides"
      ]
    },
    {
      "page": "run.lofreq.sample",
      "title": "Run LoFreq for a sample",
      "topics": [
        "run.lofreq.sample"
      ]
    },
    {
      "page": "run.muse.sample",
      "title": "Run MuSE for a sample",
      "topics": [
        "run.muse.sample"
      ]
    },
    {
      "page": "run.mutect.sample",
      "title": "Run MuTect for a sample",
      "topics": [
        "run.mutect.sample"
      ]
    },
    {
      "page": "run.post.processing",
      "title": "run.post.processing",
      "topics": [
        "run.post.processing"
      ]
    },
    {
      "page": "run.target.qc",
      "title": "Perform sample QC by looking at target coverage.",
      "topics": [
        "run.target.qc"
      ]
    },
    {
      "page": "run.target.qc.sample",
      "title": "Get ontarget reads and run coverage quality control",
      "topics": [
        "run.target.qc.sample"
      ]
    },
    {
      "page": "run.vardict.sample",
      "title": "run.vardict.sample",
      "topics": [
        "run.vardict.sample"
      ]
    },
    {
      "page": "run.variant.calling",
      "title": "run.variant.calling",
      "topics": [
        "run.variant.calling"
      ]
    },
    {
      "page": "run.varitas.pipeline",
      "title": "Run VariTAS pipeline in full.",
      "topics": [
        "run.varitas.pipeline"
      ]
    },
    {
      "page": "run.varitas.pipeline.hybrid",
      "title": "run.varitas.pipeline.hybrid",
      "topics": [
        "run.varitas.pipeline.hybrid"
      ]
    },
    {
      "page": "run.varscan.sample",
      "title": "Run VarScan for a sample",
      "topics": [
        "run.varscan.sample"
      ]
    },
    {
      "page": "save.config",
      "title": "save.config",
      "topics": [
        "save.config"
      ]
    },
    {
      "page": "save.coverage.excel",
      "title": "Save coverage statistics to multi-worksheet Excel file.",
      "topics": [
        "save.coverage.excel"
      ]
    },
    {
      "page": "save.variants.excel",
      "title": "Save variants to Excel.",
      "topics": [
        "save.variants.excel"
      ]
    },
    {
      "page": "set.varitas.options",
      "title": "Set options for varitas pipeline.",
      "topics": [
        "set.varitas.options"
      ]
    },
    {
      "page": "split.on.column",
      "title": "split.on.column",
      "topics": [
        "split.on.column"
      ]
    },
    {
      "page": "sum.dp4",
      "title": "sum.dp4",
      "topics": [
        "sum.dp4"
      ]
    },
    {
      "page": "system.ls",
      "title": "Run ls command",
      "topics": [
        "system.ls"
      ]
    },
    {
      "page": "tabular.mean",
      "title": "tabular.mean",
      "topics": [
        "tabular.mean"
      ]
    },
    {
      "page": "tabular.median",
      "title": "tabular.median",
      "topics": [
        "tabular.median"
      ]
    },
    {
      "page": "trinucleotide.barplot",
      "title": "Make barplot of trinucleotide substitutions",
      "topics": [
        "trinucleotide.barplot"
      ]
    },
    {
      "page": "variant.recurrence.barplot",
      "title": "Make barplot of variants per caller",
      "topics": [
        "variant.recurrence.barplot"
      ]
    },
    {
      "page": "variants.caller.barplot",
      "title": "Make barplot of variants per caller",
      "topics": [
        "variants.caller.barplot"
      ]
    },
    {
      "page": "variants.sample.barplot",
      "title": "Make barplot of variants per sample",
      "topics": [
        "variants.sample.barplot"
      ]
    },
    {
      "page": "verify.bam.specification",
      "title": "Check that sample specification data frame matches expected format, and that all files exist",
      "topics": [
        "verify.bam.specification"
      ]
    },
    {
      "page": "verify.bwa.index",
      "title": "verify.bwa.index",
      "topics": [
        "verify.bwa.index"
      ]
    },
    {
      "page": "verify.fasta.index",
      "title": "verify.fasta.index",
      "topics": [
        "verify.fasta.index"
      ]
    },
    {
      "page": "verify.fastq.specification",
      "title": "Check that FASTQ specification data frame matches expected format, and that all files exist",
      "topics": [
        "verify.fastq.specification"
      ]
    },
    {
      "page": "verify.sequence.dictionary",
      "title": "verify.sequence.dictionary",
      "topics": [
        "verify.sequence.dictionary"
      ]
    },
    {
      "page": "verify.varitas.options",
      "title": "Check against common errors in the VariTAS options.",
      "topics": [
        "verify.varitas.options"
      ]
    },
    {
      "page": "verify.vcf.specification",
      "title": "verify.vcf.specification",
      "topics": [
        "verify.vcf.specification"
      ]
    }
  ],
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    "stringi",
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      "source": "errors.Rmd",
      "filename": "errors.html",
      "title": "What Does This Error Mean?",
      "author": "Adam Mills",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The Purpose of This Guide",
        "Verifying VariTAS Options",
        "The following stages are not supported: ____",
        "Solution",
        "varitas.options must be a list of options or a string giving the path to the config YAML file",
        "config must include reference_build",
        "reference_build must be either grch37 or grch38",
        "Reference genome file ____ does not have extension .fa or .fasta",
        "target_panel must be provided for alignment and variant calling stages",
        "Mismatch between reference genome and target panel",
        "Index files not found for reference genome file ____ - try running bwa index.",
        "Sequence dictionary not found for file ____ - try running GATK CreateSequenceDictionary.",
        "Fasta index file not found for file ____ Try running samtools faidx."
      ],
      "created": "2020-02-21 11:00:03",
      "modified": "2020-11-13 23:30:03",
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    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "The VariTAS Pipeline",
      "author": "Erle Holgersen and Adam Mills",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Pipeline Overview",
        "Third-Party Software",
        "Directory Structure",
        "Stages",
        "Alignment",
        "Variant Calling",
        "VarDict",
        "MuTect",
        "Annotation",
        "Merging",
        "Running the Full Pipeline",
        "Updating Settings",
        "Variant Filters",
        "Solid Tumour Mode",
        "ctDNA Mode",
        "Examples and Use Cases",
        "Generic Wrapper Script",
        "Variant Calling with Matched Normal",
        "Ion PGM Data",
        "MiniSeq Data",
        "Incorporating MiniSeq Variant Calls",
        "References"
      ],
      "created": "2020-02-21 11:00:03",
      "modified": "2020-11-13 23:30:03",
      "commits": 2
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  "_indexed": true,
  "_nocasepkg": "varitas",
  "_universes": [
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