HaplotypeCaller and detection of large indels
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I am wondering about the detection of large indels with the haplotypecaller. I have an example where to my mind there is quite clearly a large deletion (a couple of kb) in the sample, but it is not called by the HaplotypeCaller.

How do I modify the parameters of HC to detect large indels? activeRegionMaxsize? indelSizeToEliminateInRefModel


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