Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

HaplotypeCaller is slow

My variant calling seems very slow. What do you think?

We have 10 BAM files, each about 2.5GB, covering a targetted region of about 15MB.

I am using the HaplotypeCaller with 8 threads (-nct 8) and it is taking 31 hours.

When we start whole genome sequencing this will be impossible!

Any ideas on how to speed things up? Is this a normal speed?

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