The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at

Emitting ref vs. alt allele counts on all sites

eranmickeranmick Member Posts: 1


I would like to use UnifiedGenotyper to produce a vcf file where all sites I specify via BED file will have a count of reads carrying the reference allele and a count of reads carrying an alternate allele, regardless of whether a variant has been called in the site.
I've tried to use EMIT_ALL_SITES, but this appears not to provide this count breakdown for sites that are not called as variable.
I would appreciate any pointers. I am using GATK 2.2.4.

Thank you very much.

Best Answer


Sign In or Register to comment.