private CanvasCallset GetCallset()
{
IFileLocation outputVcfPath = CommonOptions.OutputDirectory.GetFileLocation("CNV.vcf.gz");
CanvasCallset callSet = new CanvasCallset(
_bam,
CommonOptions.SampleName,
CommonOptions.WholeGenomeFasta,
CommonOptions.OutputDirectory,
CommonOptions.KmerFasta,
CommonOptions.FilterBed,
CommonOptions.PloidyBed,
CommonOptions.BAlleleSites,
CommonOptions.IsDbSnpVcf,
Enumerable.Empty<IFileLocation>(),
null,
null,
outputVcfPath);
return callSet;
}