I have adapted my pipeline to the new filtering strategies implemented in gatk 126.96.36.199 and while looking at its output I noticed that the stat file generated by mutect2 has a negative number:
I did not find the documentation about this file content but in the gatk forum it is mentioned that is should represent the number of bases above a certain coverage (10 by default). This happened for a WGS sample, while for WES I obtain a more sensible value (well, at least positive and integer, even if maybe a tad high):
Has this happened to anyone else? I compared the resulting calls obtained for the WGS with a previous version of mutect2 and they are comparable-ish (98% of the new "ones" are in common with the "old" ones), but I am still worried that something fishy is happening, expecially considering that the filtering step of the pipeline uses this stats file.