GATK HaplotypeCaller memory problem

[Robby]

Hello everyone,

I would like to use GATK v2.3.9 for variant calling. But unfortunally the Haplotype Caller fails with the following error message:

There was a failure because you did not provide enough memory to run this program

I used the following command for the Haplotype Caller:

java -Xmx31g -jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R reference.fasta \
-I example_realigned.bam \
--dbsnp dbsnp.vcf \
-stand_call_conf 50.0 \
-stand_emit_conf 10.0 \
-o example.raw.snps.indels.vcf

What is wrong? How can I improve the command?
Best regards

Robby

[GenoMax]

See the two links referred to in the second post of this thread: http://gatkforums.broadinstitute.org...aplotypecaller

You do have 31G+ of physical RAM available on the server/node?