Sunday, June 12, 2011

Re: [Bio-bwa-help] reporting multiple (BWA) hits as separate SAM lines

The author of BWA (Li Heng) released a perl script to convert multi-hit BWA lines.

Feature request on the Email Archive: (bio-bwa-help)

The perl script: xa2multi.pl was added to convert XA:Z tag to multiple lines (part of https://github.com/lh3/bwa).

example command: > bwa samse ref.fa reads.sai reads.fq.gz | xa2multi.pl > out.sam

(originally found Via kevin-gattaca.)