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Identification of "messy" ActiveRegions?
I've been reading the very good documentation on bamout (including https://www.broadinstitute.org/gatk/guide/article?id=5484 ), and was struck by this detail:
"In some cases HaplotypeCaller does not complete processing on an ActiveRegion that it has started. This is typically because there is either almost no evidence of variation once the remapping has been done, or on the contrary, the region is very messy and there is too much complexity."
Is there any way that we can identify the regions where HaplotypeCaller stopped because the region was too messy? We are very interested in explicitly identifying regions in our samples where a call cannot be made and, if I understood correctly, identification of regions "too messy for HaplotypeCaller" would bear directly on that.