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```
What steps will reproduce the problem?
1. bamToBed -i foo.bam -split
on the following foo.bam file
@HD VN:1.4 GO:none SO:coordinate
@SQ SN:chr9 LN:124076172
@RG ID:sample1 P…
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I am trying to compile TMAP on ubuntu but getting following error:
src/util/../seq/../io/tmap_sam_io.h:79:1: error: unknown type name ‘sam_header_t’
In file included from src/util/tmap_definitions.c:…
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@drosofff, est-ce que les workflows sont en quelque versionné ?
Comment savoir si nous ne les avons déjà pas https://usegalaxy.fr/workflows/list_published ?
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The log likelihood reported can sometimes be largely negative. My data are quite sparse TGS data, so I use a low min.het and cval. Facets complains about data quality, however the outputs are quite of…
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All throughout the pipeline, there are places that assume paired-end reads, and it's mostly how we wrap underlying tools, probably not the underlying tools themselves. For example, BAM->fastq conversi…
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I really don't want to use GATK indel realigner.
![image](https://user-images.githubusercontent.com/453972/45338661-aec8fd00-b5d1-11e8-960e-0c7e2eeb3c3e.png)
```
CP006053 1598997 . …
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Hello. I'm reporting this for [Homebrew](https://github.com/mxcl/homebrew), a package installer for OSX. We are having trouble upgrading to version 3.2.0 of tmap, and we are getting some strange unde…
2bits updated
10 years ago
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While looking at some CRAM files that had been through GATK realigner, I noticed that they included BD:Z and BI:Z aux tags. These tags do not appear in the SAMtags specification. [This GATK forums t…
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### Description of bug
This is an issue with the documentation. The [Quick start](https://github.com/ablab/spades?tab=readme-ov-file#quick-start) provides commands to test the installation, but all o…
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Hi,
I appear to be getting the following error when running the following command hybracter test-long which I presume is related to medaka. I wondered if you have encountered this issue before and …