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188 Open 105 Closed
188 Open 105 Closed
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Issues list

Set min insert size with -I option. Why do I still get proper pairs with insert size < min insert size?
#419 opened May 3, 2024 by js72587
Is there MD tag in output of bwa?
#418 opened Apr 16, 2024 by YuanHank
missing bwa-0.7.18.tar.bz2 for 0.7.18 release
#417 opened Apr 15, 2024 by chenrui333
1
Could anyone tell me the exact meaning of '-5SP'?
#416 opened Mar 21, 2024 by hanshanmengqi
no ID within the read group line
#415 opened Mar 21, 2024 by FengjuanjuanCMS
Indexing large genome failed
#413 opened Mar 14, 2024 by xzhoubayer
2
[M::bwa_idx_load_from_disk] read 0 ALT contigs
#412 opened Mar 13, 2024 by erah1
Build fails with LTO
#411 opened Feb 29, 2024 by eli-schwartz
1
When i use bwa for mapping with grch37.p13.fa and hg19.fa，there exists some differences in some regions.
#410 opened Dec 28, 2023 by zhangshouwei309194
Fail to read header from fasta input
#409 opened Dec 6, 2023 by gustavogregoracci
Did bwa index use the SA-IS algorithm?
#408 opened Nov 30, 2023 by MiyaaL
bwa mem hangs after a few thousand reads
#407 opened Nov 29, 2023 by chklee30
Reads with mapq=0 not mapped to the same location as their mates
#405 opened Nov 3, 2023 by pinbo
Output reads not paired with a mixture of single end and paired end reads when using smart-pairing
#403 opened Oct 6, 2023 by nh13
Non-text characters appearing in SEQ field
#402 opened Sep 6, 2023 by csoeder
How to interpret the meaning of flag=0 in the alignment results of BAM files generated by bwa-mem2 mem
#400 opened Sep 1, 2023 by wlhCNU
Is this an wrong alignment score in bwa-mem alignment?
#398 opened Aug 15, 2023 by huichanghuang
[mem] reads are not labelled as proper pair
#397 opened Aug 7, 2023 by ftian9
clipping penalty
#396 opened Jun 23, 2023 by FarGlasgow
bwa aln -m maximum entries in the queue not documented in manual
#394 opened Jun 7, 2023 by marykthompson
BWA BAM
#393 opened May 16, 2023 by duhuipeng
3
xa2multi.pl outputs RNEXT w.r.t. original alignment
#390 opened Apr 26, 2023 by tsnorri
1
1
Can I use Apache2 branch under Apache 2.0 license?
#389 opened Mar 29, 2023 by pasang0000
question on mapping to short reference like 1kb
#388 opened Feb 14, 2023 by jianshu93
Error coming during compilation
#387 opened Feb 11, 2023 by achintkansal
3
ProTip! What’s not been updated in a month: updated:<2024-04-08.