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# Filter references by % identity

This is a two-step filter that first determines the number of reads mapping to a reference with at least 90% identity, then identifies those references with at least 50% reads passing the first threshold. Both filter settings can be changed individually and the thresholds can also be set as upper instead of lower limits. By default all references fulfilling the filter criteria are discarded.

Note

The % identity calculation is based on information in the CIGAR string and the optional MD tag and will fail if the SAM file contains no header.

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