This is a two-step filter that calculates the post-mortem degradation score for each read and in first step determines the number of ancient reads (PMDS at least 3) mapping to a reference, then identifies those references with at least 50% reads passing the first threshold. Both filter settings can be changed individually. By default all references fulfilling the filter criteria are discarded.
Note
The PMD score calculation is based on information in the CIGAR string and the optional MD tag and will fail if the SAM file contains no header.