VarDictJava BED file input Problem
Entering edit mode
8.1 years ago
morovatunc ▴ 550


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.


VarDict WGS • 2.4k views
Entering edit mode
7.9 years ago
DG 7.3k

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.


Login before adding your answer.

Traffic: 2526 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6