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audqf 01-30-2012 02:47 PM

How to deal with no calls from GATK Unifiedgenotyper for indels
I am working with 454 single-end long-read data for a region on chr6, using hg19 and dbSNP build 135 as references. GATK Unifiedgenotyper with the option -glm INDEL returns no calls on realigned+recalibrated bam file and on recalibrated bam file. Using additional arguments, such as --output_mode EMIT_ALL_SITES, or setting call/emit thresholds, does not make a difference, either.

Earlier posts on this forum ( indicate that a high sequencing error rate may be the cause.

So I wonder:
1. If resetting the sequencing error rate is the solution, how do I do it? Is this error rate reported in the bam file?

2. Are there other ways of tweaking GATK to deal with this problem?

Thanks for your help!

ulz_peter 01-30-2012 11:43 PM

I once tried to twaek GATK to output Indels in 454 data, but I think they turned that utility off as soon as you specify the PL:454 (or maybe it was PL:ROCHE, I don't remember) tag. In case you find a solution, I'd be happy to it

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:

(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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