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Old 04-03-2013, 08:36 AM   #1
Location: Germany

Join Date: Mar 2011
Posts: 68
Default GATK HaplotypeCaller memory problem

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

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Old 04-03-2013, 10:18 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,053

See the two links referred to in the second post of this thread:

You do have 31G+ of physical RAM available on the server/node?
GenoMax is offline   Reply With Quote

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