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# [PMDtools] Filter reads by PMDS

This filter uses a modified version of PMDtools to calculate the post-mortem degradation score (PMDS) for each read and discards all reads with scores below the set threshold.

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.

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