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Outputting bamout to read post-realignment coverage including non-variants

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Hi,

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 -disableOptimizations and --emitDroppedReads, but should I also turn on --forceActive and --dontTrimActiveRegions? In addition, would these flags affect the results of the variant calling itself?

Thanks for the help!


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