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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

HaplotypeCaller takes too long

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
-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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