HaplotypeCaller Multisample Variant Calling
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Comments (6)

Hey there!

I've been using HaplotypeCaller as part of a new whole genome variant calling pipeline I'm working on and I had a question about the number of samples to use. From my tests, it seems like increasing the number of samples to run HaplotypeCaller on simultaneously improves the accuracy no matter how many samples I add (I've tried 1, 4, and 8 samples at a time). Before I tried 16 samples, I was wondering if you could tell me if there's a point of diminishing returns for adding samples to HaplotypeCaller. It seems like with every sample I add, the time/sample increases, so I don't want to keep adding samples if it's not going to result in an improved call set, but if it does improve the results I'll deal with it and live with the longer run times. I should note that I'm making this pipeline for an experiment where there will be up to 50 individuals, and of those, there are family groups of 3-4 people. If running HaplotypeCaller on all 50 simultaneously would result in the best call set, that's what I'll do. Thanks! (By the way, I love the improvements you made with 2.5!)

  • Grant

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