countAlleles: Count alleles in SV sites across samples

In jmonlong/sveval: SV evaluation

Count alleles in SV sites across samples

Description

Read a VCF file and count alleles for SVs grouped by SV site. The sv.sites parameter is a list defining which SVs are assigned to which SV site. The SV ids are those created by readSVvcf.multisamps which is expected to be run first.

Usage

countAlleles(vcf.file, sv.sites, gq.instead = FALSE)

Arguments

vcf.file	the path to the VCF file
sv.sites	a list defining the SV sites (each element contains a vector with SV ids)
gq.instead	return a matrix with the minimum genotype quality for each site instead of the allele counts. Default is FALSE.

Value

a matrix with allele counts for each site (rows) and samples (columns)

Author(s)

Jean Monlong

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