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Haplotype caller in GVCF mode still taking a very long time. Can I possibly speed up the process?

apolyakapolyak State College, PA, USAMember

I have 13 whole exome sequencing samples, and unfortunately, I'm having a hard time getting HaplotypeCaller to complete within the time frame the cluster I use allows (150 hours). I use 10 nodes at a time with 10gb ram with 8 cores per node. Is there any way to speed up this rate? I tried using HaplotypeCaller in GVCF mode with the following command:

java -d64 -Xmx8g -jar $GATKDIR/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R $REF --dbsnp $DBSNP \
-I 7-27_realigned.bam \
-o 7-27_hg19.vcf \
-gt_mode DISCOVERY \
-mbq 20 \
-stand_emit_conf 20 -G Standard -A AlleleBalance -nct 16 \
--emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000

Am I doing something incorrectly? Is there anything I can tweak to minimize the runtime? What is the expected runtime for WES on a standard setup (a few cores and some ram)?

Best Answer


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