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: [email protected]<mailto:[email protected]>
Website: www.illumina.com<http://www.illumina.com>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
