import_VCFs: import_VCFs

In pllittle/UNMASC: Tumor-Only Variant Calling with Unmatched Normal Control Samples

import_VCFs

Description

Imports Strelka VCFs containing SNVs and INDELs

Usage

import_VCFs(DAT, FILTER = NULL, ncores = 1)

Arguments

DAT	A data.frame containing column names 'FILENAME' for the full vcf filename and 'STUDYNUMBER' for a unique string mapped to the control sample used when calling variants against the same tumor.
FILTER	A list containing named elements 'nDP', 'tDP', 'Qscore', and 'contigs' for minimum normal depth, minimum tumor depth, minimum Qscore, and a string of contigs to retain, respectively. Default values are nDP = tDP = 2, Qscore = 3, and contigs = chr1-chr22, chrX, chrY.
ncores	A positive integer for the number of threads to use for calculating strand-specific read counts.

Value

A R data.frame containing vcf fields

pllittle/UNMASC documentation built on June 1, 2025, 1 p.m.