read_snp_matrix: Read counts file

In mskcc/facets-suite: Functions to run and parse output from FACETS

Read counts file

Description

Reads a gzipped output file from snp-pileup.

Usage

read_snp_matrix(input_file, err.thresh = 10, del.thresh = 10)

Arguments

input_file	Path to input file.
err.thresh	Threshold for errors at locus.
del.thresh	Threshold for deletions at locus.

Value

A SNP count matrix, with the following columns:

• Chromosome and Position: Chromosomal position of SNP.

• NOR.DP: Total read depth in normal sample.

• TUM.DP: Total read depth in tumor sample.

• NOR.RD: Reference allele read depth in normal sample.

• TUM.RD: Reference allele read depth in tumor sample.

Source

snp-pileup is part of FACETS.

mskcc/facets-suite documentation built on Sept. 13, 2022, 4:14 a.m.