How does GATK HaplotypeCaller behave with respect to deletions that span across a supplied interval in a bed file using -L?
I can't find anything in the documentation that explains whether a deletion would be included in the output VCF if it spans across the start or end point of an interval in the supplied bed file using the -L argument (i.e. part of the deletion is within the supplied region and part is not).
From the testing I have done it seems that such a deletion would not be included in the output, but I wanted to verify whether that is the case, and find out specifically where in the code or documentation this behaviour is displayed.
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