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brentp
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bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
139
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53
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YC and MD tag issue
#93
Javkhaa
opened
13 hours ago
1
Overriding hardcoded -B values is possible from command line
#92
edawson
opened
4 months ago
3
Exception("bad or empty fastqs")
#91
kea027
opened
5 months ago
2
BWA-meth mapping issues
#90
alirazzaq254
opened
6 months ago
0
when running bwameth example, exception: AttributeError: module 'toolshed.files' has no attribute 'prefunc'
#89
teryyoung
closed
7 months ago
2
repeated alignment (bwa get stuck)
#88
hanrong498
closed
8 months ago
2
escape % in help text for --do-not-penalize-chimeras to fix TypeError when using 'bwameth.py --help'
#87
boegel
closed
1 year ago
1
unrecognized reference name during sam_parse
#86
nash5202
closed
1 year ago
9
Help command for aligner command does not work
#85
slazicoicr
closed
1 year ago
1
Meet Error When running bwa meth mem2
#84
WRui
opened
1 year ago
0
Timestamp checking of .fa files prevents me from running bwa-meth in the cloud
#83
jnthnhss
opened
1 year ago
2
Q: Issues with installation 0.2.5
#82
sklages
closed
1 year ago
1
Unique mapped reads
#81
Hongxiang2023
opened
2 years ago
1
Only split "SN" from the rest of the contig name
#80
jdidion
closed
2 years ago
3
`handle_header` mangles alt contigs
#79
jdidion
closed
2 years ago
2
broken pipeline
#78
WRui
closed
2 years ago
3
bwa-mem2 cannot recognize the input from the pipe
#77
yewero
closed
2 years ago
5
bwa-meth index error
#76
almanza-d
closed
2 years ago
12
[Release Request] make a release since bwa-mem2 index are not included in current version
#75
TTTPOB
closed
2 years ago
1
The link in `README.md` of the `compare/` folder is not working
#74
xie186
closed
2 years ago
4
Fixed bug in argument checking which meant that only indexing ran
#73
chris-cheshire
closed
2 years ago
3
Output of bwa-meth in BAM format
#72
paulinehermans
closed
1 year ago
1
Support for BWA-MEM2
#71
PoisonAlien
closed
2 years ago
3
Fix typo in README
#70
paulmenzel
closed
2 years ago
0
Adding argument for not penalizing chimeric reads
#69
nchernia
closed
2 years ago
1
bam chrom name fix
#68
tsy19900929
closed
3 years ago
2
Methylcaller alternatives to recommended MethylDackel
#67
Blosberg
opened
3 years ago
1
Question: multimapping handling
#66
weedcentipede
closed
4 years ago
4
MAPQ0 due to secondary alignment in alt contigs
#65
yangruialex
opened
4 years ago
2
raise BWAMethException("first run bwameth.py index %s" % fa)
#64
sengoku93
opened
4 years ago
16
Feature request: add `bwa mem2` support
#63
xie186
closed
1 year ago
1
align without trimming for quality and/or adaptor
#62
crazyhottommy
closed
5 years ago
2
Why is there a problem?
#61
yubau1112
closed
5 years ago
1
YC and YD tags
#60
alexpcheng
opened
5 years ago
0
Mapping Rate From bwa-meth
#59
groverj3
closed
5 years ago
7
Do not add RG by default
#58
okartal
opened
5 years ago
2
unique bam?
#57
MoutonAlice
closed
5 years ago
1
toolshed issue
#56
supermaxiste
closed
6 years ago
9
Mapq
#55
nchernia
opened
6 years ago
5
Does bwa-meth aligned bam files need to be duplicates marked for downstream methylDackel work properly?
#54
crazyhottommy
closed
6 years ago
1
error with bwa-mem -R
#53
crazyhottommy
closed
6 years ago
1
c2t: don't exhaust memory when input files aren't interleaved.
#52
grahamgower
closed
6 years ago
1
Methylation data
#51
nchernia
closed
6 years ago
6
-p flag
#50
nchernia
closed
6 years ago
2
Handle reads on stdin
#49
bwlang
closed
6 years ago
4
bwameth can't handle stdin input
#48
bwlang
closed
6 years ago
5
Interleaved support
#47
bwlang
closed
6 years ago
7
add support for interleaved PE fastq
#46
bwlang
closed
6 years ago
1
Fix default read group to respect SAM spec
#45
nsoranzo
closed
6 years ago
1
bwameth set_as_failed=args.set_as_failed
#44
jrmerritt6
opened
6 years ago
6
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