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:dan@bx.psu.edu]
Sent: Wednesday, September 07, 2011 10:57 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
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 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: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,

Dan

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}" "gatk_input_${i}"

       -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

    --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}"

    --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}"

Ilya Chorny Ph.D.

Bioinformatics Scientist I

Illumina, Inc.

9885 Towne Centre Drive

San Diego, CA 92121

Work: 858.202.4582

Email: ichorny@illumina.com

Website: www.illumina.com