HaplotypeCaller speed
Posted in Ask the GATK team | Last updated on 2012-09-10 15:30:14

Comments (44)


how does the speed of the haplotypeCaller usually compare to that of the UnifiedGenotyper?

When I try to use it, it seems to be about 90x slower.

these are the command lines I use:

java -jar -Xmx32g GenomeAnalysisTK.jar -R hg19.fasta -T UnifiedGenotyper -dcov 1000 -I file.bam -o file.vcf -L myTarget

java -jar -Xmx32g GenomeAnalysisTK.jar -R hg19.fasta -T HaplotypeCaller -dcov 1000 -I file.bam -o file.vcf -L myTarget


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