lh3 bwa issues - Githubissues

lh3 / bwa

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

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bwa index of 300GB multifasta fails at bwt2sa stage without error

#436 hazmup closed 1 month ago
3
one end of paired end reads disappeared in the aligned BAM file

#435 sotuamax opened 1 month ago
0
After running make，I did not see ref.fa

#434 tudousiZzz opened 2 months ago
0
Sequence mapping only when complement

#433 7PintsOfCherryGarcia closed 2 months ago
0
No matching manifest for linux/arm64/v8 in the manifest list entries

#432 DrDinhLuong opened 2 months ago
0
discarding reads which contains too many mismatches

#431 nicolo-tellini opened 3 months ago
0
Cannot allocate memory

#430 emilyhokning opened 3 months ago
0
feature proposal: allow tag name to be specified for storing fastq comment for read

#429 bpow closed 3 months ago
1
unexpected high quality scores with chimeric SA alternatives reported

#428 Dmitry-Antipov closed 3 months ago
3
How can i obtain all the regions reads hit. (in duplication region)

#427 liukeweiaway closed 3 months ago
2
fixed a compiler error

#426 kemin711 opened 4 months ago
0
Continuation after error "paired reads have different names"

#425 scg40 opened 4 months ago
1
BWA and short read mapping

#424 alessandromacc opened 4 months ago
0
the significance of the -V parameter and XR tag

#423 YettaWang opened 4 months ago
0
How are ambiguity charaters handled in BWA?

#422 SaitouAsuka opened 5 months ago
0
Fixed a bug on shm existence checking when there are indice more than two.

#421 wook-choi closed 5 months ago
0
bwa alignment of Nanopro sequences to call the transposable elements (TEs)

#420 Anees-caas opened 5 months ago
0
Set min insert size with -I option. Why do I still get proper pairs with insert size < min insert size?

#419 js72587 opened 6 months ago
0
Is there MD tag in output of bwa?

#418 YuanHank opened 7 months ago
0
missing `bwa-0.7.18.tar.bz2` for 0.7.18 release

#417 chenrui333 opened 7 months ago
1
Could anyone tell me the exact meaning of '-5SP'?

#416 hanshanmengqi opened 8 months ago
0
no ID within the read group line

#415 FengjuanjuanCMS opened 8 months ago
0
Fix `kt_for()` declaration parameter types

#414 jmarshall opened 8 months ago
0
Indexing large genome failed

#413 xzhoubayer opened 8 months ago
3
[M::bwa_idx_load_from_disk] read 0 ALT contigs

#412 erah1 opened 8 months ago
0
Build fails with LTO

#411 eli-schwartz opened 9 months ago
0
When i use bwa for mapping with grch37.p13.fa and hg19.fa，there exists some differences in some regions.

#410 zhangshouwei309194 opened 11 months ago
0
Fail to read header from fasta input

#409 gustavogregoracci opened 11 months ago
0
Did bwa index use the SA-IS algorithm?

#408 MiyaaL opened 12 months ago
0
bwa mem hangs after a few thousand reads

#407 chklee30 opened 12 months ago
0
how to eliminate the effects of estimated insertion size distribution

#406 Ben-unbelieveable closed 1 year ago
1
Reads with mapq=0 not mapped to the same location as their mates

#405 pinbo opened 1 year ago
0
Question about XA Tag and MAPQ Values

#404 zqlns closed 1 year ago
1
Output reads not paired with a mixture of single end and paired end reads when using smart-pairing

#403 nh13 opened 1 year ago
0
Non-text characters appearing in SEQ field

#402 csoeder opened 1 year ago
0
Time to release new version?

#401 Yikun closed 7 months ago
8
How to interpret the meaning of flag=0 in the alignment results of BAM files generated by bwa-mem2 mem

#400 wlhCNU opened 1 year ago
0
The bwa index is faulty

#399 heweihuang closed 1 year ago
0
Is this an wrong alignment score in bwa-mem alignment?

#398 huichanghuang opened 1 year ago
0
[mem] reads are not labelled as proper pair

#397 ftian9 opened 1 year ago
0
clipping penalty

#396 FarGlasgow opened 1 year ago
0
bwa mem different result in repetitive test

#395 baoyl818 closed 1 year ago
1
bwa aln -m maximum entries in the queue not documented in manual

#394 marykthompson opened 1 year ago
0
BWA BAM

#393 duhuipeng opened 1 year ago
3
Left-most alignment of gaps?

#392 eranbio closed 1 year ago
1
Fix RNEXT output in xa2multi.pl

#391 tsnorri opened 1 year ago
0
xa2multi.pl outputs RNEXT w.r.t. original alignment

#390 tsnorri opened 1 year ago
1
Can I use Apache2 branch under Apache 2.0 license?

#389 pasang0000 opened 1 year ago
0
question on mapping to short reference like 1kb

#388 jianshu93 opened 1 year ago
0
Error coming during compilation

#387 achintkansal closed 2 months ago
5