extract_variants_from_vcf_file {musicatk} | R Documentation

## Extracts variants from a vcf file

### Description

Add Description

### Usage

    extract_variants_from_vcf_file(
      vcf_file,
      id = NULL,
      rename = NULL,
      sample_field = NULL,
      filename_as_id = FALSE,
      strip_extension = c(".vcf", ".vcf.gz", ".gz"),
      filter = TRUE,
      multiallele = c("expand", "exclude"),
      extra_fields = NULL,
      fix_vcf_errors = TRUE
    )

### Arguments

`vcf_file` | Path to the vcf file
`id` | ID of the sample to select from VCF. If `NULL`, then the first sample will be selected. Default `NULL`.
`rename` | Rename the sample to this value when extracting variants. If `NULL`, then the sample will be named according to `ID`.
`sample_field` | Some algoriths will save the name of the sample in the ##SAMPLE portion of header in the VCF (e.g. ##SAMPLE=<ID=TUMOR,SampleName=TCGA-01-0001>). If the ID is specified via the `id` parameter ("TUMOR" in this example), then `sample_field` can be used to specify the name of the tag ("SampleName" in this example). Default `NULL`.
`filename_as_id` | If set to `TRUE`, the file name will be used as the sample name.
`strip_extension` | Only used if `filename_as_id` is set to `TRUE`. If set to `TRUE`, the file extention will be stripped from the filename before setting the sample name. If a character vector is given, then all the strings in the vector will removed from the end of the filename before setting the sample name. Default `c(".vcf",".vcf.gz",".gz")`
`filter` | Exclude variants that do not have a `PASS` in the `FILTER` column of the VCF. Default `TRUE`.
`multiallele` | Multialleles are when multiple alternative variants are listed in the same row in the vcf. One of `"expand"` or `"exclude"`. If `"expand"` is selected, then each alternate allele will be given their own rows. If `"exclude"` is selected, then these rows will be removed. Default `"expand"`.
`extra_fields` | Optionally extract additional fields from the `INFO` section of the VCF. Default `NULL`.
`fix_vcf_errors` | Attempt to automatically fix VCF file formatting errors.

### Value

Returns a data.table of variants extracted from a vcf

### Examples

    vcf <- system.file("extdata", "public_LUAD_TCGA-97-7938.vcf",
      package = "musicatk")
    variants <- extract_variants_from_vcf_file(vcf_file = vcf)

[Package musicatk version 1.2.0 Index]