Prepare data for impute
generate.impute.input.wgs.germline(
chrom,
germline.allele.counts.file,
normal.allele.counts.file,
output.file,
imputeinfofile,
is.male,
problemLociFile = NA,
useLociFile = NA,
heterozygousFilter = 0.1
)The chromosome for which impute input should be generated.
Output from the allele counter on the matched germline for this chromosome.
Output from the allele counter on the matched normal for this chromosome.
File where the impute input for this chromosome will be written.
Info file with impute reference information.
Boolean denoting whether this sample is male (TRUE), or female (FALSE).
A file containing genomic locations that must be discarded (optional).
A file containing genomic locations that must be included (optional).
The cutoff where a SNP will be considered as heterozygous (default 0.01).