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How to interpret results from GATK ApplyVQSR

kittyskittys BirminghamMember
Hello,

I am currently following the GATK v4 best practises pipeline for short germline variant calling. The final step is applying a variant quality recalibration model to the output vcf file, using different tranche sensitivity values. However the documentation for this is very unclear and I am struggling to identify which variants are the ones I want to keep - are the ones labelled as PASS ones I want to select? Or the ones that contain tranche values?

The only clue I can find in old documentation is that ones labelled as "filtered" should be discarded - but this word doesn't appear anyway in my output file. Could the documentation be updated for version 4 to make this clearer to use for other users too?

Any help is massively appreciated!!

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