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Issues list

bwa index of 300GB multifasta fails at bwt2sa stage without error
#436 by hazmup was closed Oct 16, 2024
3
Sequence mapping only when complement
#433 by 7PintsOfCherryGarcia was closed Sep 11, 2024
feature proposal: allow tag name to be specified for storing fastq comment for read
#429 by bpow was closed Aug 20, 2024
1
unexpected high quality scores with chimeric SA alternatives reported
#428 by Dmitry-Antipov was closed Aug 7, 2024
3
How can i obtain all the regions reads hit. (in duplication region)
#427 by liukeweiaway was closed Aug 12, 2024
2
how to eliminate the effects of estimated insertion size distribution
#406 by Ben-unbelieveable was closed Nov 6, 2023
1
Question about XA Tag and MAPQ Values
#404 by zqlns was closed Nov 6, 2023
1
Time to release new version?
#401 by Yikun was closed Apr 15, 2024
8
The bwa index is faulty
#399 by heweihuang was closed Aug 22, 2023
bwa mem different result in repetitive test
#395 by baoyl818 was closed Aug 7, 2023
1
Left-most alignment of gaps?
#392 by eranbio was closed May 12, 2023
1
Error coming during compilation
#387 by achintkansal was closed Sep 25, 2024
5
bwa mem ont2d
#375 by Oksanak22 was closed Oct 12, 2022
2
Trailing whitespace in SAM file
#371 by dylanlawrencebio was closed Aug 26, 2022
2
tied matches of bwa and bowtie2
#370 by jianshu93 was closed Aug 22, 2022
1
bwa mem fails to identify paired-end sequences with 'not enough pairs' message
#357 by cokelaer was closed Oct 16, 2024
6
how to attach XM tag
#352 by S-111 was closed May 4, 2022
1
improper read pair status given; for pairs falling outside insert size boundaries for low complexity amplicon library
#350 by alexander-e-f-smith was closed Apr 29, 2022
1
Question about mate rescue and MAPQ. The same alignments, different results
#340 by shenghuanjie was closed Jan 27, 2022
1
bwa mem - fastq sequence order
#338 by Fazulur was closed Dec 27, 2021
2
bwa-mem PE mode: reads mapping to repetitive regions are being non randomly assigned?
#333 by fburden44 was closed Oct 28, 2021
1
PACBIO contigs with BWA-MEM
#329 by khush876 was closed Jun 29, 2021
2
Migrate Travis CI by May 31, 2021
#324 by junaruga was closed May 10, 2021
1
Wrong SAM file header generated with BWA -mem option
#323 by stachyris was closed May 15, 2021
4
Debug flag does not seem to do anything
#320 by ghuls was closed Mar 9, 2021
1
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