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:
I used the following command for the Haplotype Caller:
What is wrong? How can I improve the command?
Best regards
Robby
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
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
-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
Best regards
Robby
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