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Old 02-01-2012, 03:53 PM   #3
audqf
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Location: Chicago

Join Date: Jan 2012
Posts: 2
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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.
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