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Outputting bamout to read post-realignment coverage including non-variants
I want to output a bamout to see the post-realignment coverage (a la
-A DepthPerAlleleBySample) for a position, regardless of whether that site is a variant site. I'm sure I'm need to turn on
--emitDroppedReads, but should I also turn on
--dontTrimActiveRegions? In addition, would these flags affect the results of the variant calling itself?
Thanks for the help!