read a INFO tag in the VCF/BCF into R data structure

Usage

vcfinfo(
  vcffile,
  tag,
  region = "",
  vartype = "all",
  ids = NULL,
  qual = 0,
  pass = FALSE,
  setid = FALSE
)

Arguments

vcffile: path to the VCF/BCF file
tag: the INFO tag to extract.
region: region to subset in bcftools-like style: "chr1", "chr1:1-10000000"
vartype: restrict to specific type of variants. supports "snps","indels", "sv", "multisnps","multiallelics"
ids: character vector. restrict to sites with ID in the given vector. default NULL won't filter any sites.
qual: numeric. restrict to variants with QUAL > qual.
pass: logical. restrict to variants with FILTER = "PASS".
setid: logical. reset ID column as CHR_POS_REF_ALT.

Value

Return a list containing the following components:

chr: : character vector;
the CHR column in the VCF file
pos: : character vector;
the POS column in the VCF file
id: : character vector;
the ID column in the VCF file
ref: : character vector;
the REF column in the VCF file
alt: : character vector;
the ALT column in the VCF file
qual: : character vector;
the QUAL column in the VCF file
filter: : character vector;
the FILTER column in the VCF file
tag: : vector of either integer, numberic or character values depending on the tag to extract;
a specifiy tag in the INFO column to be extracted

Details

vcfinfo uses the C++ API of vcfpp, which is a wrapper of htslib, to read VCF/BCF files. Thus, it has the full functionalities of htslib, such as restrict to specific variant types, samples and regions. For the memory efficiency reason, the vcfinfo is designed to parse only one tag at a time in the INFO column of the VCF. Currently it does not support parsing a vector of values for a given INFO tag.

Author

Zilong Li zilong.dk@gmail.com

Examples

library('vcfppR')
vcffile <- system.file("extdata", "raw.gt.vcf.gz", package="vcfppR")
res <- vcfinfo(vcffile, "AF", region = "chr21:1-5050000", vartype = "snps", pass = TRUE)
str(res)