This wrapper for a modified version of PMDtools does not have any filter functionality but simply calculates the post-mortem degradation score for each read and writes it into a custom DS tag by running the command
pmdtools_mod --dry --writesamfield --header
Following PMDtools steps in the workflow will utilize these tags and skip the calculation to save time.
PMDtools can only calculate post-mortem degradation scores for SAM files which contain a complete header with CIGAR strings and optional MD tags because it has to reconstruct the reference sequence from these fields. The tool can optionally write a brief statistical summary to the Messages dock when done, however this is disabled by default.
See also
Skoglund et al. (2014) for details on the calculation of post-mortem degradation scores and the original version of PMDtools.