Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Notable changes:
(0.7.18: 14 April 2024, r1243)
This release adds option -q to preserve the mapping quality of split alignment with a lower alignment score than the primary alignment. Option -5 automatically applies -q as well. BWA outputs identical alignments to the previous version unless option -5 is used.
(0.7.17: 23 October 2017, r1188)
This release added a couple of minor features and incorporated multiple pull requests, including:
Added option -5, which is useful to some Hi-C pipelines.
Fixed an error with samtools sorting (#129). Updated download link for GRCh38 (#123). Fixed README MarkDown formatting (#70). Addressed multiple issues via a collected pull request #139 by @jmarshall. Avoid malformatted SAM header when -R is used with TAB (#84). Output mate CIGAR (#138).
(0.7.16: 30 July 2017, r1180)
This release fixes a few minor bugs in the previous version and adds a few minor features. All BWA algorithms should produce identical output to 0.7.12 when there are no ALT contigs.
Detailed changes:
(0.7.13: 23 Feburary 2016, r1126)