5.2 years ago by
Following on a little from Brian's answer, the threshold you would choose depends on where you want to make your precision/sensitivity tradeoff. In an ideal world you could work out expected precision/sensitivity directly from the probabilities represented by the QUAL or GQ scores but in practise those scores are not well calibrated. If you do have a gold-standard call-set for your sample, you can use RTG Tools (free) or RTG Core (free for non-commercial use) from our website, it makes running the comparison and seeing the effects of different thresholds very easy:
rtg vcfeval -t ref -b gold-.vcf.gz -c calls.vcf.gz -o eval-GQ
rtg vcfeval -t ref -b gold.vcf.gz -c calls.vcf.gz -f QUAL -o eval-QUAL
rtg vcfeval -t ref -b gold-.vcf.gz -c calls.vcf.gz -f INFO=VQSLOD -o eval-GQ # if you have run VQSR
rtg rocplot eval-*/weighted_roc.tsv.gz
The last command brings up a gui containing the ROC curves for comparison and using a slider you can see the effects of applying a threshold on your sensitivity / precision.