Question concerning GATK VQSR recalibration
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5 days ago
balaena ▴ 10

Hi everyone,

I have a question concerning the GATK best practice: after joint genotyping, VQSR recalibration is performed via the resource bundle (e.g. hapmap, 1000G, etc). The resulting vcf file has some variants labelled "PASS" and some are labelled e.g. VQSRTrancheSNP99.90to100.00. As far as I understand those are considered false positives.

Is it fine to only include variants that have been labelled "PASS" in the downstream analysis?

Thanks a lot and best regards!

WGS GATK VQSR WES analysis genome • 94 views
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