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!