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