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

In vcfppR: Rapid Manipulation of the Variant Call Format (VCF)

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

Description

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.

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.

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

Author(s)

Zilong Li [e-mail]

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)

vcfppR documentation built on Aug. 25, 2025, 5:11 p.m.