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I have 15 exome-seq samples, and have been using BWA-PiCard-GATK pipeline to do the variant calling. I did not realize GATK is so slow until I have to analyze this large number of samples. In this HaplotypeCaller step, each sample seems to take at least 2 days (48+ hours). Is this normal is there's something I did wrong? Below is my command, is there anything wrong or GATK-HaplotypeCaller is known this slooooow?
java -Xmx10g -Djava.awt.headless=true -jar
-T HaplotypeCaller \
-minPruning 3 \
-dcov 10 \
-R ./GATK_ref/hg19.fasta \
-I ./GATK/BQSR/sample1_realign.recal.compressed.bam \
Is there anything I did wrong with this command? or anything I can change to make it run faster? I am using GATK 2.5 by the way. thanks!