GATK update changes UnifiedGenotyper output

[doc.ramses]

Hey,

recently I upgraded to the latest version (GenomeAnalysisTK-1.2-1-g33967a4) and I noticed that when I run the UnifiedGenotyper with standard settings, I don't get the "SB" value, that I need for hard-filtering. When I ran the UG of the previous version with standard settings, I got it.
How can I set for this parameter in the new version ?

Cheers!

[Bukowski]

GATK 1.2 release notes: http://www.broadinstitute.org/gsa/wi...TK_release_1.2

From release notes:

"SB annotation is no longer calculated by default; use --computeSLOD to turn it on. Users should check out the FS annotation for a Fisher's exact test of strand bias."

[doc.ramses]

Thank you for pointing this out!