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Old 07-01-2015, 01:24 AM   #3
Location: Quadraro, Rome

Join Date: Jul 2012
Posts: 11

Hi Linnea, and thanks for the very quick reply!

I actually found out a similar answer on the GATK forum after I posted it, but yours was concise and very explanatory, so thank you again!

I'm now running the --bamOutput option on my samples in order to check ho HaplotypeCaller realigned the reads.

However, something still does not add up, specifically, why the GenotypeQuality (GQ) of these Indels is always 99 (checked multiple times on multiple samples)?

Thanks in advance!


Last edited by wariobrega; 07-01-2015 at 01:30 AM.
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