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Old 11-29-2013, 05:32 AM   #1
mboursnell
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Location: Cambridge, UK

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Question Speed of variant callers

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 GATK 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?
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Old 11-29-2013, 05:42 AM   #2
dpryan
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You'll really want to follow Brad Chapman's blog. He writes a lot about various algorithm comparisons and also works on bcbio, which is probably what you're really looking for (see an associated blog post of his here).
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Old 11-29-2013, 01:18 PM   #3
shi
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Quote:
Originally Posted by mboursnell View Post
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 GATK 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?

The exactSNP is a lot faster. And it has at least comparable performance from our experience.
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Old 12-04-2013, 02:25 AM   #4
mboursnell
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OK, thanks. I'll try exactSNP. How did you do the comparison between exactSNP and GATK?
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Old 12-04-2013, 12:26 PM   #5
shi
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We are now preparing the manuscript for exactSNP. A preprint should be available early next year.
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Old 12-04-2013, 04:10 PM   #6
adamyao
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If you have pair-end fastq files you can upload them to HiPipe directly (http://hipipe.ncgm.sinica.edu.tw/). HiPipe powered by 640 cores can do alignment (BWA) and variant calling (GATK) very fast. A human exome (70X-100X) can be processed in 2 hrs excluding upload time.
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