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HaplotypeCaller takes too long

rcholicrcholic DenverMember

I'm running the latest GATK nightly build to process human exome-seq data (has 12 samples). It seemed be faster than the older version until I run the HaplotypeCaller. The run summary shows it will take 14 days to finish. I am wondering if there's anything in my below command: How to make it faster without losing data in the output?

java -Xmx10g -Djava.io.tmpdir=/temp/GATK_temp
-jar $CLASSPATH/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R ../GATK_ref/hg19.fasta \
-I ./compressedbam.list \
-L ../GATK_ref/hg19knownGene_UCSC_sorted.bed \
-log ../GATK/VQSR/log/HaplotypeCaller_20131018.log \
-o ../GATK/VQSR/raw.snps_indels.vcf


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