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### Task Description
In PR #1727 we moved a number of terms into a single `local` cv as described here:
> At some point in the history of Tripal, we created a number of chado table focused cvs (…
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Dear Byron,
First of, I wanted to thank you for developing this great piece of software. We are really excited to use it coupled with the metagenotypes generated from GT-Pro.
We are trying to de…
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I generated vcf's from MANTA then annotated them using AnnotSV tool. then tried running vcf2circos tool i get this error :
>> $ vcf2circos --input output.vcf --options Static/options.json --output ou…
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Hi @eugenegardner just wondering what the consequences of not applying any filter for the ALT/ALT genotypes would be. Very likely including false positive calls? Also do you have any idea why is this …
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I noticed on the [Basic Operations][0] wiki page that there are two types of genotypers contained within `vg`: `vg call` and `vg genotype`. The documentation on the "Basic Operations" page notes that…
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For the command generator to be organized into a protocol-module structure similar to other sections, this ticket will outline its current status and some potential caveats.
Current status:
There …
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I'm not so sure about that name but it seems like the most obvious choice given how our other counting functions are named.
This should do what https://scikit-allel.readthedocs.io/en/stable/model/n…
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The minimum kmer coverage parameter is used to define a threshold where a kmer is present or absent. Minimizer kmers with coverage less than this threshold are considered absent, and these absent kmer…
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As part of clarifying the documentation I am trying to understand what does `-nophasefounders` option do so we can write better docs!?
The docs say `A flag phase a heterozygous allele in one of the…
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Hi guys,
I'm trying VIVA with .vcf file generated with MANTA software and I got this message:
> Welcome to VIVA.
>
> Loading dependency packages:
>
> ┌ Warning: ORCA.jl has been deprecated…