GetAlleleCounts: for input variant calls and genotypes, return genotype...

In Halvee/rvatk: Rare Variant Analysis Toolkit

Description

for input variant calls and genotypes, return genotype counts, taking into account the chromosome and sample gender for each variant call. For example, a 'homozygous' on an x chromosome of a male would be an allele count of only 1, rather than 2, whereas a female homozygous call on an x chromosome would be an allele count of 2.Such rules do not apply to autosomes, where each sample should have two copies of each.

Usage

GetAlleleCounts(sample.ID, variant.ID, genotype, sampleped)

Arguments

sample.ID	vector of samples IDs
variant.ID	vector of variant IDs
genotype	vector of genotype strings (het / hom)
sampleped	data frame of samples in sampleped format

Halvee/rvatk documentation built on May 6, 2019, 10:55 p.m.