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?



From: Daniel Blankenberg []
Sent: Wednesday, September 07, 2011 10:57 AM
To: Chorny, Ilya
Subject: Re: GATK Unified Genotyper

Hi Ilya,

The JVM can be quite a pain when determining the best way to determine max 
memory, however the underlying 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:DefaultMaxRAMFraction' of 2 
(half of ram) - future enhancements to the tool running code will allow this to 
be set based upon e.g. number of jobs and available ram per node (no time frame 
for this).

It does look like num_threads/nt is now available for the UnifiedGenotyper. 
Many of the GATK tools list it as an available parameter, but when run will 
give an error saying it is not yet implemented (only can determine by trial and 
error or reading source code). I've updated the Unified Genotyper to use 
--num_threads 4. Thanks!

It might be a good idea to coordinate the changes you are looking into with 
GATK with the changes we are approaching. Any other feedback would also be 
greatly appreciated.

Thanks for using Galaxy,


On Sep 7, 2011, at 1:25 PM, Chorny, Ilya wrote:

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 slow  on human data.

--stdout "${output_log}"
   #for $i, $input_bam in enumerate( $reference_source.input_bams ):
       -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" 
       -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" 
"gatk_input_${i}" ##hardcode galaxy ext type as bam_index
   #end for
   -p 'java -Xmx3g
    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
    -T "UnifiedGenotyper"
    -o "${output_vcf}"
    ##-o "out_vcf.txt"
    -et "NO_ET" ##ET no phone home
    ##-log "${output_log}" ##don't use this to log to file, instead directly 
capture stdout
    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"
    #end if
    -nt 3

Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582

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