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Old 04-24-2012, 05:21 PM   #1
caswater
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Location: Canada

Join Date: Jun 2011
Posts: 47
Default dubious SNP calls from GATK

Hi, I followed the Best Practice v3 steps and called SNPs with GATK. After having the raw SNPs, I used VQSR to recalibrate and post-filter the reported raw SNPs. However, the trenches plot from VQSR recalibration looks like below:



which indicates that even if I used the recommended cutoff to refine the SNPs, I still get a lot false positives.

My data are just standard Illumina data, my analysis just followed GATK Best Practice v3. Do you have this problem before, and how shall I solve this issue?

Thanks a lot
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