bwa mem -w option
0
0
Entering edit mode
5.9 years ago
ibseq12 • 0

does anybody know what is the range of INT that can be used for the -w option of BWA Mem? (-w ) : INTBand width. Essentially, gaps longer than *INT will not be found. Note that the maximum gap length is also affected by the scoring matrix and the hit length, not solely determined by this option. [100]

thanks ib

Assembly • 1.3k views
ADD COMMENT
0
Entering edit mode

Just guessing, but isn't this the maximum gap length within a read to be reported in the same hit. Longer than this and the read alignment will be split and reported in a separate hit/line

ADD REPLY

Login before adding your answer.

Traffic: 1369 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6