prep_UNMASC_VCF: prep_UNMASC_VCF

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

prep_UNMASC_VCF

Description

A comprehensive function to import VCFs, annotations, and target bed file to prepare the necessary VCF for UNMASC's main workflow.

Usage

prep_UNMASC_VCF(
  outdir,
  DAT,
  FILTER,
  target_fn,
  anno_fn,
  nlines = 100,
  ncores = 1
)

Arguments

outdir	A character string of the full path and working directory specifying where intermediate and final files are stored.
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.
target_fn	A filename for the tab delimited target capture bed file. The first three column headers should be 'Chr', 'Start', and 'End'.
anno_fn	A filename for the unique set of variant loci called across multiple normals and annotated by VEP.
nlines	An integer specifying the number of initial lines to read in from the anno_fn to assess the expected formatting.
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 and annotation.

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