SEQanswers - View Single Post - How to deal with no calls from GATK Unifiedgenotyper for indels

audqf · 02-01-2012, 03:53 PM

In case ulz_peter and others are interested, it turns out that GATK UG does not make indel calls for 454 data.

I also posted the same question here:
http://getsatisfaction.com/gsa/topic...#reply_7912928

(btw, this is a pretty good place to have GATK-related questions answered)

Now the wiki page for GATK UG clearly states this limitation:
http://www.broadinstitute.org/gsa/wi...fied_genotyper

Hope this helps. I'm trying samtools for indel calling now.

02-01-2012, 03:53 PM	#3
audqf Junior Member Location: Chicago Join Date: Jan 2012 Posts: 2	In case ulz_peter and others are interested, it turns out that GATK UG does not make indel calls for 454 data. I also posted the same question here: http://getsatisfaction.com/gsa/topic...#reply_7912928 (btw, this is a pretty good place to have GATK-related questions answered) Now the wiki page for GATK UG clearly states this limitation: http://www.broadinstitute.org/gsa/wi...fied_genotyper Hope this helps. I'm trying samtools for indel calling now.