dcov on a BAM file to generate BAM file output
Trying to get a question in before the shutdown. Is everything shutting down in the US....
I am trying to do a dcov to say 100X coverage (note that I want a fixed depth, not a fraction downsampling) and get the resulting reads in a BAM file. Getting the reads resulting from the dcov in the output file is the key thing here.
I have tried this with both PrintReads (which seemed the obvious choice) and with IndelRealigner but both seem to ignore the dcov argument passed to the GATK engine and write the whole of the input BAM to the output BAM.
Does anyone know which tool could be used to carry out this task?