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.
GenotypeGVCFs remaining runtime estimate incorrect
I have noticed when using the GenotypeGVCFs walker (version 3.2), that the remaining runtime estimate is very poor. The estimate from CombineGVCFs and other walkers on the other hand is very accurate. This is not a critical bug. It is rather a feature enhancement. I just noticed that the "completed" percentage is also incorrect. It does not start at 0%. In fact it has stayed constant after walking over 2 million base pairs of 2000 samples in 2 hours. I am not using multi threading. Not that important to me, but I thought I would let you know.