Active Region Re-assembly
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How do I turn off local re-assembly in active regions? Is this even possible?
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I wanted to follow up with more information regarding this question.
Although we do not have a way to turn off the active region re-assembly, there may be a way to solve the issue you are having with HaplotypeCaller in other ways. One possible solution is to use the option --alleles, which calls a give site regardless of evidence. You can also use the -bamout option to look at the resulting BAM file after reassembly and see what is going on at that site.
We have a troubleshooting document that is very helpful for figuring out HaplotypeCaller results: https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant
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Hello Ellen Weinheimer, active region re-assembly is a main part of HaplotypeCaller so we have no option to turn it off. However, there are many HaplotypeCaller settings that you can try out for optimizing results. See the tool documentation here: https://gatk.broadinstitute.org/hc/en-us/articles/360046787532-HaplotypeCaller
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