MapQualityCutoff

From Array Suite Wiki

Specifies the minimal mapping quality allowed for an alignment to be included in the calculation.

Alignments with mapping quality below this value will be ignored.

Value must be between 0 and 255.


Note: Starting from 09/10/2013, mapping quality in the OSA BAM file uses the following:
MAX (1, 60/(NH * (NM+ 1)) )

Many public alignment tools automatically set mapping quality to 255 to indicate that mapping quality was not used. Previously, OSA aligner did not produce mapping quality and set mapping quality to 255 like other aligners. BWA is another aligner that produces mapping quality.

NH: Number of hits of the reads (if the reads can only be uniquely mapped to reference, then NH=1, if it can be mapped to multiple position then NH>1 which lower the mapping quality)

NM: Number of mismatch of the reads.