private CanvasCallset GetCallset(ILogger logger)
{
IFileLocation outputVcfPath = CommonOptions.OutputDirectory.GetFileLocation("CNV.vcf.gz");
var manifest = new NexteraManifest(_manifest.FullName, null, logger.Error);
CanvasCallset callSet = new CanvasCallset(
_tumorNormalOptions.TumorBam,
CommonOptions.SampleName,
CommonOptions.WholeGenomeFasta,
CommonOptions.OutputDirectory,
CommonOptions.KmerFasta,
CommonOptions.FilterBed,
CommonOptions.PloidyBed,
CommonOptions.BAlleleSites,
CommonOptions.IsDbSnpVcf,
new[] { _normalBam },
manifest,
_tumorNormalOptions.SomaticVcf,
outputVcfPath);
return callSet;
}