Question: BWA-mem MAPQ Calculation
4
gravatar for rfriedman22
2.0 years ago by
rfriedman2240
Washington University in St. Louis
rfriedman2240 wrote:

How does BWA-mem calculate mapping quality (MAPQ) for a given read? I've seen plenty of posts discussing how this is done in BWA, but not using BWA-mem. Is the MQ simply a scale between 0 and 60 (what appears to be the maximum)? Or do certain values have certain meaning? For example, I know in Bowtie2 certain MAPQ values correspond to reads that have one best match (i.e. AS > XS), but is not a simple scale where a larger number corresponds to higher quality ( http://biofinysics.blogspot.com.au/2014/05/how-does-bowtie2-assign-mapq-scores.html ).

ADD COMMENTlink modified 4 days ago by h.mon16k • written 2.0 years ago by rfriedman2240

Tagging: lh3

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by genomax52k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1879 users visited in the last hour