I wanted to make this part of my pipeline quicker and use the Sparked version of RevertSam. However, there is no Max_Discard_Fraction option (which is funny since the GATK pipelines for realigning BAM files uses it). The parameter essentially tells the program to quit if a high enough fraction of reads are gotten rid of with the sanitize option.

I set it at 0.005, whereas the default is 0.01. Is it fine to go on without this option? I'm also curious on general feelings about Spark versions of tools