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  • jtrivino
    Junior Member
    • Feb 2011
    • 4
    #1

    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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