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Picard 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the github release page for download and details.

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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Answers

  • 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

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    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_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @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.

  • Maybe I should stick to UnifiedGenotyper?

  • Sounds good. I'll look forward to it

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