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Old 05-06-2011, 03:28 AM   #1
jtrivino
Junior Member
 
Location: Valencia

Join Date: Feb 2011
Posts: 4
Default SNPs false positive GATK

Hi

I have used GATK for SNPs calling in Solid platforms of a sample with a deep coverage. I have realigned and recalibrated as the pipeline of GATK literature. The result is in general good, but in a SNPs I have had a value of QD of 1 and don't pass the last filter of SNPs, I know that this SNPs is a flase negative,Can I eliminate the QD of the SNPs filter?, QD depends of deep coverage?

Thanks!
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