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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
Post edited by Geraldine_VdAuwera on