X-ons

QTLTools

1) "filter-mapping-quality"    "Minimal phred mapping quality for a read to be considered.")
2) "filter-mismatch"                "Maximum mismatches allowed in a read. If between 0 and 1 taken as the fraction of read length. (Requires NM attribute)")
3) "filter-mismatch-total"      "Maximum total mismatches allowed in paired reads. If between 0 and 1 taken as the fraction of combined read length. (Requires NM attribute)")
4) "check-proper-pairing"      "If provided only properly paired reads according to the aligner that are in correct orientation will be considered. Otherwise all pairs in correct orientation will be considered.")
5) "check-consistency"           "If provided checks the consistency of split reads with annotation, rather than pure overlap of one of the blocks of the split read.")