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### MAVIS version:
### Python version:
### OS:
## Expected Behaviour
SAMTools check success / no error
## Actual Behaviour
I'm finding reports like the following in the output logs in the…
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I've been using the USeq application AlignmentEndTrimmer to trim and filter RNAseq datasets for detection of A-to-I RNA editing, and I noticed that this application cannot process reads on chrX. Every…
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I think most of the query types are quite simple but I think it would be more friendly to have a one sentence title or description above each type. For example the "Coding exons" type could have some…
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Hello, @roryk !
Thanks for the great pipeline!
After upgrading to 1.0.5 stable version, and also upgrading with --datatarget rnaseq,
I encountered an error:
```
2017-10-26T16:24Z] Annotati…
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- Intron branch point data is not showing (was showing in old browser)
- Variation track is missing
- track selector filter for "curated sequence and features" for forward/reverse strand + genome…
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This package needs to deal with the extra information that SLiM stores in a tree sequence, reading it easily, and creating it in tree sequences lacking it. These are defined [here](https://github.com…
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Dear @bioconda/all,
to create the author list of the Bioconda paper, we need your full name and affiliation (include address). I hope to be able to include everybody who is part of the github team, p…
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Hello,
Is it possible to use a GFF file for the annotations instead of a GTF file?
Or do you know of any good means of converting between these two formats?
Kind regards,
John Hellgren
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Hi guys -
Following up on #2242 (where the issue was due to GATK 4.0.0.0 vs. 4.0.1.0) and #2189 (where I wasn't able to get the multithreaded version of HaplotypeCaller going, I'm now hitting the…
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Hi,
I have a VCF file with some INFO fields encoded with `Number=A.` `VariantAnnotation::readVcf` works fine, but `VariantAnnotation::readVcfAsVRanges` does not work (_Error: is(values, "vector_OR_…