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: icho...@illumina.com<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>
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