The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
positive and negative set in model training by variantRecalibrator
Thanks for develop this tool set and share with others with good supports, it really contains a lot of wonderful tools.
I just try to understand VQSR more into detail. If I give the resources (dbsnp, hap map and 1kg omni data) recommended by the best practice with default settings (which one is in training, which one is the true set ...), Does the positive set contain all variants which recorded in the resources having train=TRUE, but how does the tool select negative set? Does it order the variants from high to low by the QUAL value, and pick up the 5% from the bottom (if the percentBad = 0.05)? Will there be some overlap between positive set and negative set? And is there any quality filtration on the data, e.g. one date point is more than a standard deviation away from average...