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lh3
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bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
GNU General Public License v3.0
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Add the header line to the output SAM
#336
nh13
closed
2 years ago
1
bwa mem not set proper pair flag
#335
Frank1219
opened
3 years ago
2
Reads aligning to hard masked regions with Ns
#334
hp2048
opened
3 years ago
0
bwa-mem PE mode: reads mapping to repetitive regions are being non randomly assigned?
#333
fburden44
closed
3 years ago
1
Moved source files to src
#332
Stefan-Schroder
closed
2 years ago
0
Not an issue but hopefully usefull for Dockerized bwa. Alpine base image segfaults.
#331
markotitel
opened
3 years ago
0
Add the mate mapping quality tag
#330
nh13
closed
2 years ago
1
PACBIO contigs with BWA-MEM
#329
khush876
closed
3 years ago
2
bwa_mem
#328
123123456abc
opened
3 years ago
0
Resume
#327
ardy20
opened
3 years ago
0
flag settings for perfect-matched alignments
#326
zhenzhenyang-psu
opened
3 years ago
0
Use GitHub Actions instead of Travis CI
#325
jmarshall
closed
3 years ago
1
Migrate Travis CI by May 31, 2021
#324
junaruga
closed
3 years ago
0
Wrong SAM file header generated with BWA -mem option
#323
stachyris
closed
3 years ago
4
Reads with chastity filter set
#322
Poshi
opened
3 years ago
0
SAM parsing error: Incomplete line
#321
siqi-zZ
opened
3 years ago
0
Debug flag does not seem to do anything
#320
ghuls
closed
3 years ago
1
Version Release Update Request
#319
dorton21
closed
3 years ago
0
Fail to index human genome in a shell with 120Gb memory
#318
yangyxt
opened
3 years ago
2
Allow specifying of in_3.fastq
#317
ghuls
closed
3 years ago
1
Cpp compatability
#316
starling13
closed
2 years ago
0
bwa compile failed at utils.c:29:10
#315
sagitaninta
opened
3 years ago
1
BWA compile fail with GCC 10
#314
fizwit
opened
3 years ago
6
bwa index problem when indexing files with large size
#313
544728460
opened
3 years ago
8
Freebsd and hurd compatibility
#312
mr-c
opened
3 years ago
0
Fix some typos
#311
mr-c
opened
3 years ago
0
BWA indexing of human genome very long runtime
#310
dkioroglou
closed
3 years ago
2
Convert "properly read" constants to command line parameters
#309
gdgib-roche
opened
3 years ago
1
mem_process_seqs: fix redundant memory allocation
#308
starling13
opened
3 years ago
0
Installation: No rule ... stop messages
#307
mdhar1980
opened
3 years ago
2
no alignments to chrY
#306
rturba
opened
3 years ago
0
~
#305
wulj2
closed
3 years ago
0
Is the license to bwa MIT or GPLv3?
#304
nh13
closed
4 years ago
2
zlib.h
#303
TianyuLee
opened
4 years ago
0
Question: how single-end and pair-end alignment mode affect AS score
#302
liu-xingliang
closed
4 years ago
0
Log verbosity
#301
ghost
closed
2 years ago
2
Does not compile for ARM
#300
mattchatporter
opened
4 years ago
14
How BWA determine a paired-end read is proper or improperly paired?
#299
NTNguyen13
closed
4 years ago
1
the flag of bam
#298
tyyiyi
opened
4 years ago
1
Clarify bwa mem -5 option
#297
nh13
closed
2 years ago
0
Increasing the 5' clipping penalty drops alignments with no 5' clipping
#296
nh13
opened
4 years ago
0
Support 0 length qual in fastq
#295
d-cameron
opened
4 years ago
0
allow the user to specify the XA drop ratio via the -z option
#294
nh13
closed
2 years ago
0
Output mapping quality with XB
#293
nh13
closed
2 years ago
0
Document "-u"
#292
nh13
closed
2 years ago
2
change strlen to seq->name.l
#291
lindenb
opened
4 years ago
0
paired end read name problems
#290
dpellow
opened
4 years ago
1
BWAKit run-gen-ref can't get files for resource-GRCh38
#289
jtm732
opened
4 years ago
1
Remove some unused variables
#288
ilkerg
opened
4 years ago
0
Average Coverage Calculator for bwakit hg38
#287
DarioS
opened
4 years ago
0
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