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# HaplotypeCaller is slow

Posts: 94

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?

Tagged:

• Posts: 23

Hello,

It doesn't sound unusual in my experience - I've run HaplotypeCaller with 94 samples after ReduceReads, nct 20, minPruning 2. I paralellized it - running two jobs with nct 20, 1 Mb at a time for each thread. A chromosome in my species is ~14 Mb, and that took about 2-3 days. I would say running a couple jobs and decreasing the size of your target segment for each job might help, since then variant calling won't stall completely on difficult regions?

YW

That seems like a lot, although it sounds like that's pretty deep sequencing. Maybe you're running into coverage issues. Are you using ReduceReads to compress your data at all?

Geraldine Van der Auwera, PhD

@leeyoungwha, the runtimes you're getting sounds about right, but you're working with 94 samples; whereas Mike is working with only 10, which should be comparatively much faster.

Geraldine Van der Auwera, PhD

• Posts: 94

Maybe I should stick to UnifiedGenotyper?

• Posts: 94

Sounds good. I'll look forward to it