Hello all,
one of my users encounters a strange error with the GATK tool "Unified
Genotyper". At the end of the message you see the original error report. The
problem there was that the reference genome is missing. The tool was run as a
part of a bigger workflow, but I double checked the workfl
Hi Ilya,
Something similar to this is planned, but directly referencing location files
is being deprecated in favor of using the tool_data_tables mechanism. The
validator implementation does not yet support data tables, but will be enhanced
in the future. Additionally, the selection functional
To prevent user error in mixing genomes, would you be interested in a feature
in which the unified genotyper choses the genome in a fashion similar to how
samtools know which which genome to use?
Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illum
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 sugg
The newest version of the Unified Genotyper has a -glm option which needs to be
set to both to call indels.
BTW, any interest in writing a wrapper for the Depth of Coverage tool?
Thanks,
Ilya
From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Wednesday, September 07, 2011 10:57 AM
To: Ch
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 'XX:Defau
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 really
