minialign icon indicating copy to clipboard operation
minialign copied to clipboard

Published 20 hours ago • verified publisher icon ocxtal

Broken CIGAR string

Open ocxtal opened this issue 8 years ago • 0 comments

This is a self issue report.

Setting relatively large mismatch penalty respect to gap open penalty, such as -a1 -b3 -p1 -q1, sometimes results in broken CIGAR strings in the output SAM file. This is probably due to a bug in the alignment routine but the exact reason is not identified yet.

Please use the default (-a1 -b2 -p2 -q1) or some -a1 -b1 -p1 -q1 values to avoid this bug.

Hajime Suzuki

ocxtal avatar Nov 28 '16 14:11 ocxtal