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Similar to #9 but I can't solve it with regex. I downloaded the nextstrain tree (Jan 4, 2021) for nCov and wanted to run TreeToReads.py with it (newick attached below). However the seq-gen part give…
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Dear hyphy community:
I'm a new one to use hyphy and going to use BUSTED-MH to estimate positive selection anaysis.
However, it runs too slowly, is there any ideas to push the running? BTW, my …
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After initial talk with @ahwagner , I should move `variant.definingContext.expressions` into `variant.members`. For CIViC variants, the genomic hgvs expression should already be there.
![Screensho…
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Hi, about a year ago @hyunminkang mentioned that there would have been an upgrade on the genotyping strategy.
It seems nothing has happened (?)
Has anyone tried genotyping on 10x data to deconvo…
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We noticed that some references didn't format well and that it always happened when there was a consortium in the author list. Also, the consortium name was missing.
There is always the solution o…
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http://openreview.net/pdf?id=Sk-oDY9ge
> Learning tasks such as those involving genomic data often poses a serious challenge:
> the number of input features can be orders of magnitude larger than …
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Is it currently possible in pysamstats to generate consensus variation stats for paired end reads? As far as I can tell if a mismatch is on both reads for a given position, it gets counted twice.
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Write a script to apply the user's filter selections to an annotated VCF.
Input parameters:
- _Filters_: command-line arguments describing the user's filter selections, e.g. "filters=clinsig:patho…
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Hi Quentin
I haven't managed to find any information about how IGoR handles allelic variants presented in models. In default models some IGHV, TRAV and TRBV genes have several alleles (up to 7) and…
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### Contribution guidelines
- [X] I've read the [contribution guidelines](https://github.com/squidfunk/mkdocs-material/blob/master/CONTRIBUTING.md) and wholeheartedly agree
### I've found a bug and …