SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK UnifiedGenotyper not calling any variants krobasky Bioinformatics 7 10-25-2012 11:19 PM
How to deal with no calls from GATK Unifiedgenotyper for indels audqf Bioinformatics 2 02-01-2012 03:53 PM
GATK UnifiedGenotyper calling way too many SNPs in vcf swbarnes2 Bioinformatics 0 08-17-2011 02:33 PM
GATK UnifiedGenotyper SNP calling with Agilent 50Mb target enrichment nullalleles Genomic Resequencing 1 07-18-2011 07:28 AM
missing header information in bam cause GATK unifiedgenotyper fail foxyg Bioinformatics 3 11-11-2010 10:37 AM

Reply
 
Thread Tools
Old 10-18-2011, 04:48 AM   #1
doc.ramses
Member
 
Location: Planet Earth

Join Date: Jan 2011
Posts: 26
Default GATK update changes UnifiedGenotyper output

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!
doc.ramses is offline   Reply With Quote
Old 10-18-2011, 05:23 AM   #2
Bukowski
Senior Member
 
Location: UK

Join Date: Jan 2010
Posts: 390
Default

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."
Bukowski is offline   Reply With Quote
Old 10-18-2011, 07:41 AM   #3
doc.ramses
Member
 
Location: Planet Earth

Join Date: Jan 2011
Posts: 26
Default

Thank you for pointing this out!
doc.ramses is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:10 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO