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Old 01-30-2012, 02:47 PM   #1
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Location: Chicago

Join Date: Jan 2012
Posts: 2
Default 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!
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