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Old 02-01-2012, 03:53 PM   #3
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:

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

Now the wiki page for GATK UG clearly states this limitation:

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