Hi Ilya,
--genotype_likelihoods_model / -glm is available under advanced options for the
tool; it can be set to both, snp or indel. This parameter might be pulled out
from the advanced options heading and placed on the base options in the future
to make it easier to access. Thanks for the
Hi Daniel,
I have been implementing the GATK unified genotyper and I was having some
issues. Occasionally I would get an error that the Java virtual machine would
not start. I got around that by adding the Xmx3g parameter to the command line.
I also added the -nt 3 because otherwise it's
Hi Ilya,
The JVM can be quite a pain when determining the best way to determine max
memory, however the underlying gatk_wrapper.py script was updated last week in
5970:20215fcf6da7 to allow using -Xmx or XX:DefaultMaxRAMFraction. Each of the
GATK tools are currently already set to use
