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Alignments differ between the x86_64 and arm64 builds under a non-default -A (match score)

Status: Open.

#297 In bwa-mem2/bwa-mem2;

· BenjaminDEMAILLE opened on Jul 19, 2026

SegFault aligning reads longer than fasta sequences?

Status: Open.

#296 In bwa-mem2/bwa-mem2;

· Kaddea opened on May 29, 2026

Alignment issues encountered with large genomes(>20G)

Status: Open.

#294 In bwa-mem2/bwa-mem2;

· linyuiz opened on Apr 15, 2026

Using bwa mem2 with the -r "@RG ...." creates a technically invalid BAM

Status: Open.

#293 In bwa-mem2/bwa-mem2;

· tfenne opened on Apr 2, 2026

CI workflow ready to add after Apple Silicon PR merges

Status: Open.

#291 In bwa-mem2/bwa-mem2;

· nh13 opened on Mar 20, 2026

Excessive memory usage

Status: Open.

#286 In bwa-mem2/bwa-mem2;

· adthrasher opened on Jan 13, 2026

Reference genome size in output log

Status: Open.

#285 In bwa-mem2/bwa-mem2;

· dariober opened on Jan 12, 2026

Incorrect PACKAGE_VERSION for v2.3

Status: Open.

#283 In bwa-mem2/bwa-mem2;

· sxpl-DavidSchmidt opened on Dec 10, 2025

Static builds

Status: Open.

#282 In bwa-mem2/bwa-mem2;

· bartgrantham opened on Nov 10, 2025

invalid index created

Status: Open.

#280 In bwa-mem2/bwa-mem2;

· bwlang opened on Oct 18, 2025

MQ tags are present in sam files after bwa-mem runs, but are absent in bwa-mem2.

Status: Open.

#278 In bwa-mem2/bwa-mem2;

· Alexandra2022kzn opened on Oct 1, 2025

supplementary alignments used for liftover

Status: Open.

#277 In bwa-mem2/bwa-mem2;

· mashiahdavidson opened on Jul 15, 2025