generate.impute.input.wgs: Prepare data for impute

In shaghayeghsoudi/Battenberg_customized: Battenberg subclonal copy number caller

Description

Prepare data for impute

Usage

generate.impute.input.wgs(
  chrom,
  tumour.allele.counts.file,
  normal.allele.counts.file,
  output.file,
  imputeinfofile,
  is.male,
  problemLociFile = NA,
  useLociFile = NA,
  heterozygousFilter = 0.1
)

Arguments

chrom	The chromosome for which impute input should be generated.
tumour.allele.counts.file	Output from the allele counter on the matched tumour for this chromosome.
normal.allele.counts.file	Output from the allele counter on the matched normal for this chromosome.
output.file	File where the impute input for this chromosome will be written.
imputeinfofile	Info file with impute reference information.
is.male	Boolean denoting whether this sample is male (TRUE), or female (FALSE).
problemLociFile	A file containing genomic locations that must be discarded (optional).
useLociFile	A file containing genomic locations that must be included (optional).
heterozygousFilter	The cutoff where a SNP will be considered as heterozygous (default 0.01).

Author(s)

dw9, sd11

shaghayeghsoudi/Battenberg_customized documentation built on Feb. 13, 2022, 4:10 a.m.