Bwa Versions Save

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

v0.7.18

1 month ago

Notable changes:

  • Support ARM64 (#359)
  • Output SAM header line (#336)
  • Added the XB tag to output alignment score and mapping quality
  • Fixed a compiling error with GCC 10 (#267)
  • Avoid potential buffer overflow (#232)

(0.7.18: 14 April 2024, r1243)

v0.7.17

6 years ago

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)

v0.7.16

6 years ago

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)

v0.7.15

7 years ago
  • Fixed a long existing bug which potentially leads underestimated insert size upper bound. This bug should have little effect in practice.
  • In the ALT mapping mode, this release adds the "AH:*" header tag to SQ lines corresponding to alternate haplotypes.

v0.7.13

8 years ago

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:

  • Fixed a bug in "bwa-postalt.js". The old version may produce 0.5% of wrong bases for reads mapped to the ALT contigs.
  • Fixed a potential bug in the multithreading mode. It may occur when mapping is much faster than file reading, which should almost never happen in practice.
  • Changed the download URL of GRCh38.
  • Removed the read overlap mode. It is not working well.
  • Added the ropebwt2 algorithm as an alternative to index large genomes. Ropebwt2 is slower than the "bwtsw" algorithm, but it has a permissive license. This allows us to create an Apache2-licensed BWA (in the "Apache2" branch) for commercial users who are concerned with GPL.

(0.7.13: 23 Feburary 2016, r1126)