Issues
- 3
- 2
Exception("bad or empty fastqs")
#91 opened by kea027 - 8
bwa-meth and samtools flagstat
#42 opened by anusurendra - 16
- 0
BWA-meth mapping issues
#90 opened by alirazzaq254 - 2
when running bwameth example, exception: AttributeError: module 'toolshed.files' has no attribute 'prefunc'
#89 opened by teryyoung - 7
Mapping Rate From bwa-meth
#59 opened by groverj3 - 2
repeated alignment (bwa get stuck)
#88 opened by hanrong498 - 8
IOError: Paired End Reads
#32 opened by NicolaLady - 1
- 1
Feature request: add `bwa mem2` support
#63 opened by xie186 - 1
Output of bwa-meth in BAM format
#72 opened by paulinehermans - 1
Help command for aligner command does not work
#85 opened by slazicoicr - 1
Q: Issues with installation 0.2.5
#82 opened by sklages - 9
unrecognized reference name during sam_parse
#86 opened by nash5202 - 0
Meet Error When running bwa meth mem2
#84 opened by WRui - 2
Timestamp checking of .fa files prevents me from running bwa-meth in the cloud
#83 opened by jnthnhss - 1
Unique mapped reads
#81 opened by Hongxiang2023 - 2
`handle_header` mangles alt contigs
#79 opened by jdidion - 3
broken pipeline
#78 opened by WRui - 5
bwa-mem2 cannot recognize the input from the pipe
#77 opened by yewero - 12
bwa-meth index error
#76 opened by almanza-d - 9
toolshed issue
#56 opened by supermaxiste - 1
[Release Request] make a release since bwa-mem2 index are not included in current version
#75 opened by TTTPOB - 4
- 1
- 4
Question: multimapping handling
#66 opened by weedcentipede - 2
- 2
- 1
Why is there a problem?
#61 opened by yubau1112 - 0
YC and YD tags
#60 opened by alexpcheng - 2
Do not add RG by default
#58 opened by okartal - 1
unique bam?
#57 opened by MoutonAlice - 6
Methylation data
#51 opened by nchernia - 5
- 5
bwameth can't handle stdin input
#48 opened by bwlang - 1
Does bwa-meth aligned bam files need to be duplicates marked for downstream methylDackel work properly?
#54 opened by crazyhottommy - 1
error with bwa-mem -R
#53 opened by crazyhottommy - 2
- 1
add support for interleaved PE fastq
#46 opened by bwlang - 6
bwameth set_as_failed=args.set_as_failed
#44 opened by jrmerritt6 - 1
--prefix spec in docs breaks bwameth due to new opts pass through functionality
#35 opened by swingingsimian - 5
SNP Question
#43 opened by tantrev - 21
samtools not found
#41 opened by anusurendra - 1
- 2
WARNING: 5355 reads with length < 80: this program is designed for long reads.
#39 opened by HelloYiHan - 1
- 4
README update, confused about output
#36 opened by evanbiederstedt - 2
Push out a new release?
#33 opened by dpryan79 - 2
unmapped reads in c2t converted
#28 opened by jklughammer