-snvIndelFiles

[gneedle1]

If I'm using a vcf as my -SVinputFile, but want to use -snvIndelFiles, would I just use the same vcf for both inputs?

[lgmgeo]

You can use the same VCF if you have SV AND SNV/indel in the same VCF. But it seems strange to me.

The best is 1 VCF with the SV from your sample + 1 VCF with the SNV/indel from your sample.

-SVinputFile:                   Path of the input file (VCF or BED) with SV coordinates

-snvIndelFiles:                 Path of the VCF input file(s) with SNV/indel coordinates used for false positive discovery
                                Use counts of the homozygous and heterozygous variants