VarDictJava BED file input Problem

Question

[morovatunc]

Hi,

I have WGS dataset which are based on TGCA tumor normal samples. I have to call somatic mutations with various callers. So far, I have called mutations with Somatic Sniper, Mutest and VarScan. For VarDict, It has been required a BED file for specifying regions.

I want to be consistent with my method, I have to check mutations in whole sample instead of a given region. Therefore is there a way to call mutations without giving specific regions as an input?

Thank you for your help.

Tunc.

Answer 1

[DG]

No, VarDictJava requires either a BED file or a region passed in with the -R option. You have a couple of options when working with WGS data. One would be to restrict yourself to just genes/exons and using an appropriate definition file to pass in as the BED regions file. If you really want to call intergenic mutations you could generate a BED file that broke the whole genome into regions of some size, but that covers the whole genome, and pass that in.