BetterRMDup fails when processing MALT’ed files. This is actually a bug of
the SAM parsing library used in BetterRMDup that does not handle the custom MALT
@mm record properly. The bug has been reported and will be fixed in a future
version.
SAMtools view complains about inconsistency of the sequence length when
compared to the CIGAR string. This is a bug in MALT 0.0.12 that has been
reported. Please re-MALT your files with a newer version or remove the
affected reads manually.