When running GATK 4.0.0.0, (in this case using Apply BQSR) the notice
11:36:10.430 INFO ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 1
appears. A bit of digging led me to the Python code in the newly distributed gatk program. There, there are two variables that set -Dsamjdk.compression_level=1 by default. I changed the level here to 5, but the output from ApplyBQSR remained the same, and from the file sizes i'm seeing (though I may be wrong), it seems that the compression level is not at 5.
Thoughts?
