vcfppR (version 0.8.0)

vcfinfo: 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
)

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

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.

Author

Zilong Li

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.

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)