Variant identification and frequency tallies

Variant identification and frequency tallies

Usage

variant_ID(file, panel = NULL, GT_cutoff = 0, VAF_cutoff = 0)

Arguments

file

path to the h5 file

panel

name of prebuilt panel/txdb

GT_cutoff

Fraction of cells that are successfully genotyped for initial filtering (default 0.2, meaning 20%)

VAF_cutoff

Fraction of cells that are mutated for initial filtering of variants (default 0.005, meaning 0.05%)

Value

A dataframe with each variant on a row, and tally of the number of cells that are WT, Het, Hom or missing for a mutation. Calculated VAF and gentoyping freuqency is also provided. If multiple samples are present in the h5 file, a list object will be returned with each sample as an entry in the list