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Old 11-04-2011, 01:55 PM   #1
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Location: USA

Join Date: Jan 2011
Posts: 105
Default Trouble with making indel calls using UnifiedGenotyper

I'm working with 100bp Illumina Paired end, and I have been following the GATK best practices v3.

First, I mapped with BWA.
In INDEL mode, UnifiedGenotyper returns nothing.
Second, stampy.
In INDEL mode, only one large indel, and it was a false positive.

When doing base recalibration I did not have a list of known sites. Could this be such a significant problem that UG would return nothing?
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