lh3/bwa

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

Stars: 1.8k
Forks: 581
Open beginner issues: 0
Indexed issues: 75

Dominant language: C
License: GPL-3.0
Last GitHub push: Aug 7, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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75 open issues indexed

BWA-MEM crashes with GCC 15.2 at -O2/-O3 in mem_sam_pe(); aggregate initialization avoids the crash Open

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

lh3/bwa#458 · Opened Aug 28, 2026
Security: Command Injection via kopen() pipe execution (RCE) Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

lh3/bwa#456 · Opened Jun 1, 2026
As increase (float) -n, get some additional alignments Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

lh3/bwa#454 · Opened Apr 6, 2026
massive threads slow down Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lh3/bwa#447 · 4 comments · 2 reactions · Opened Oct 10, 2025
xa2multi.pl issue creating secondary alignments from hard-clipped primary Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lh3/bwa#446 · Opened Jul 9, 2025
small genome index error Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lh3/bwa#445 · Opened Jul 4, 2025
Fail to read header from fasta input Open

Data needed

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lh3/bwa#409 · 1 comment · Opened Dec 6, 2023
bwa mem hangs after a few thousand reads Open

Data needed

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lh3/bwa#407 · Opened Nov 29, 2023
Reads with mapq=0 not mapped to the same location as their mates Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

lh3/bwa#405 · Opened Nov 3, 2023
Output reads not paired with a mixture of single end and paired end reads when using smart-pairing Open

Bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lh3/bwa#403 · 1 comment · Opened Oct 6, 2023
Is this an wrong alignment score in bwa-mem alignment? Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

lh3/bwa#398 · Opened Aug 15, 2023
bwa mem failed to locate index files Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

lh3/bwa#386 · 2 comments · 3 reactions · Opened Feb 8, 2023
bwa mem -a and -t options are incompatible? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lh3/bwa#382 · Opened Jan 3, 2023
mapping on subset of a bigger reference gives different results Open

Data needed

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lh3/bwa#381 · Opened Jan 3, 2023
Adding chm13 option in bwakit Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lh3/bwa#364 · Opened Aug 5, 2022
T2T-CHM13 index file not recognized Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lh3/bwa#363 · Opened Aug 2, 2022
Different alignment numbers to same reference sequence Open

Data needed

Difficulty 4/5 3-5 days Newbie friendliness 20/100

lh3/bwa#360 · Opened Jul 5, 2022
bwa aln returning less alignments for higher number of mismatches Open

bwa-aln Investigation needed

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lh3/bwa#358 · 4 comments · Opened Jun 23, 2022
install bwa 0.7.17 in alpine docker image Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lh3/bwa#353 · 1 comment · Opened May 5, 2022
bwa: bntseq.c:428: bns_fetch_seq: Assertion `*beg <= mid && mid < *end' failed. Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

lh3/bwa#347 · 1 comment · Opened Mar 15, 2022
postalt.js MAPQ 0 on both chr17 and Alternate Contigs Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lh3/bwa#342 · 1 comment · 2 reactions · Opened Feb 18, 2022
Increasing the 5' clipping penalty drops alignments with no 5' clipping Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lh3/bwa#296 · Opened Aug 19, 2020
Deletion at the end of the alignment Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lh3/bwa#280 · 1 comment · Opened Apr 24, 2020
BWA Kit uses an outdated version of BWA Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

lh3/bwa#268 · Opened Feb 10, 2020
BWA stuck on this sequence? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lh3/bwa#261 · 3 comments · Opened Dec 4, 2019
assertion in bntseq fails Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lh3/bwa#258 · Opened Nov 18, 2019
bwakit/run-gen-ref not checking NCBI checksums Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

lh3/bwa#257 · Opened Oct 22, 2019
fail to locate the index Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lh3/bwa#244 · Opened Jul 3, 2019
Segmentation fault Open

Data needed

Difficulty 4/5 3-5 days Newbie friendliness 20/100

lh3/bwa#240 · Opened May 7, 2019
[bwa_index] Pack FASTA... *** buffer overflow detected *** Open

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

lh3/bwa#239 · 4 comments · 1 reaction · Opened Apr 16, 2019
Some Alignments Have Impossible Flag Values Open

Difficulty 2/5 1-3 hours Newbie friendliness 30/100

lh3/bwa#235 · 1 comment · 1 reaction · Opened Feb 13, 2019
NH tag Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lh3/bwa#211 · 4 comments · 1 reaction · Opened Jul 30, 2018
bwa mem - memory usage with paired reads vs single reads Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

lh3/bwa#208 · Opened Jun 13, 2018
bwa mem -a option Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lh3/bwa#206 · Opened Jun 4, 2018
EOF marker is absent. The input is probably truncated.[bam_header_read] invalid BAM binary header (this is not a BAM file) Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

lh3/bwa#200 · Opened May 10, 2018
Patch proposals for interactively working with BWA Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

lh3/bwa#199 · 1 reaction · Opened May 9, 2018
Sai file was created but having 0 size Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lh3/bwa#196 · 2 comments · 1 reaction · Opened Apr 20, 2018
Testing practices Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

lh3/bwa#193 · Opened Apr 16, 2018
How can I get the exact match? Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

lh3/bwa#191 · 1 comment · Opened Apr 8, 2018
Update bwakit release Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

lh3/bwa#189 · 1 comment · Opened Apr 4, 2018
Please enhance documentation on the recommended use of the BWA MEM -M and -Y option Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lh3/bwa#188 · 5 comments · Opened Apr 3, 2018
Minimum score threshold (`-T` option) is not applied to paired reads Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lh3/bwa#187 · 5 comments · 2 reactions · Opened Apr 1, 2018
"Failed to locate index" despite indexing Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lh3/bwa#186 · Opened Mar 26, 2018
bwa -R <@RG> induces issue in @PG Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

lh3/bwa#185 · 1 reaction · Opened Mar 21, 2018
[W::sam_read1] parse error at line 1 Open

Difficulty 4/5 3-5 days Newbie friendliness 15/100

lh3/bwa#184 · 2 comments · Opened Mar 19, 2018
Throw out reads in the alignment? Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

lh3/bwa#180 · Opened Feb 23, 2018
Recommendations about bwa / alt contigs for TNXB/RCCX/MHC class III missing from IMGT/HLA Open

Difficulty 5/5 Over a week Newbie friendliness 18/100

lh3/bwa#179 · Opened Feb 13, 2018
bwa aln: bwa-0.7.15 SAI file not generated Open

Stale

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lh3/bwa#177 · Opened Feb 8, 2018
how to make bwa search the entire reference sequence? Open

Difficulty 4/5 3-5 days Newbie friendliness 32/100

lh3/bwa#176 · Opened Jan 22, 2018
NIH download URL for GRCh38 moved Open

Difficulty 1/5 Under an hour Newbie friendliness 48/100

lh3/bwa#175 · 1 comment · 1 reaction · Opened Jan 19, 2018

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