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-   -   SNPs false positive GATK (http://seqanswers.com/forums/showthread.php?t=11178)

jtrivino 05-06-2011 04:28 AM

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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