hets: Simple het "caller" meant to be used at validated het SNP...

In mskilab/skitools: Various mskilab R utilties

Simple het "caller" meant to be used at validated het SNP sites for tumor / normal pairs

Description

hets() outputs a tsv file of ALT ($alt.count.t, $alt.count.n) and REF ($ref.count.t,, $ref.count.n) read counts to out.file for a tumor / normal pair across a set of sites specified by an input VCF

Usage

hets(
  tum.bam,
  norm.bam = NULL,
  out.file,
  vcf.file,
  chunk.size1 = 1000,
  chunk.size2 = 100,
  mc.cores = 1,
  verbose = TRUE,
  na.rm = TRUE,
  filt.norm = TRUE
)

Arguments

tum.bam	string path to tumor sample, input to Bamfile()
norm.bam	string path to normal sample, input to Bamfile()(optional) (default = NULL)
out.file	string path to TSV output file to be generated
vcf.file	string path to VCF file of sites (eg hapmap or 1000G) at which to compute read counts
chunk.size1	integer Number of variants to process from VCF file at a time (default = 1e3)
chunk.size2	integer Number of variants to access from BAM file in a single iteration (default = 1e2)
mc.cores	integer Number of cores in mclapply (default = 1)
verbose	boolean Flag to increase verbosity (default = TRUE)
na.rm	logical Flag to remove rows with NA counts (default = TRUE)
filt.norm	logical Flag to remove any sites that have allele fraction of 0 or 1 or NA in MAF; if TRUE will remove any sites that have allele fraction 0 or 1 or NA in MAF

Value

nil

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.