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# [PMDtools] Filter reads by % identity

This filter is a wrapper for a modified version of PMDtools that targets reads with insufficient identity to their respective reference sequence. Any reads with identity values below the set minimum threshold (default is 0.95 = 95%) will be discarded.

Note

The calculation of identity according to PMDtools ignores indels, possibly deaminated bases as well as unknown bases (Ns). In order to achieve compatibility with MALT and other tools that include all of these in their calculation the three corresponding options have to be activated.

PMDtools can only calculate identity values 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 the original version of PMDtools.

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