readSVvcf.multisamps: Read SVs from a VCF file

In jmonlong/sveval: SV evaluation

Read SVs from a VCF file

Description

Read a VCF file that contains SVs for multiple samples and create a GRanges with population estimates.

Usage

readSVvcf.multisamps(
  vcf.file,
  keep.ins.seq = FALSE,
  keep.ref.seq = FALSE,
  check.inv = FALSE,
  keep.ids = FALSE,
  out.fmt = c("gr", "df"),
  min.sv.size = 10
)

Arguments

vcf.file	the path to the VCF file
keep.ins.seq	should it keep the inserted sequence? Default is FALSE.
keep.ref.seq	should it keep the reference allele sequence? Default is FALSE.
check.inv	should the sequence of MNV be compared to identify inversions.
keep.ids	keep variant ids? Default is FALSE.
out.fmt	output format. Default is 'gr' for GRanges. Other options: 'df' for data.frame.
min.sv.size	the minimum size of the variant to extract from the VCF. Default is 10

Details

Alleles are split and, for each, column 'ac' reports the total allele count. The number of "ref" genotypes, i.e. homozygous refs e.g. '0/0', and the number of called samples (not missing './.') are also counted. The 'af' column contains an estimate of the allele frequency.

Value

depending on 'out.fmt', a GRanges or a data.frame with relevant information.

Author(s)

Jean Monlong

Examples

## Not run: 
svs.gr = readSVvcf.multisamps('svs.vcf')

## End(Not run)

jmonlong/sveval documentation built on July 31, 2023, 7:50 p.m.