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 /Library/Java/Extensions/GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -minPruning 3 \ -dcov 10 \ -R ./GATK_ref/hg19.fasta \ -I ./GATK/BQSR/sample1_realign.recal.compressed.bam \ -o ./GATK/VQSR/sample1_realign.raw.snps_indels.vcf
What other variant calling program do you guys recommend? Can I use the above sample1_realign.recal.compressed.bam file (prepared by GATK procedures before HaplotypeCaller) for use with the program you recommend? Thank you
ps: GATK 2.5 is what I am using.
No other variant caller tool is as "good" as GATK HaplotypeCaller (written 2014-05-21) that I know. If someone finds a better tool, please reply here.