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Hi,
If I called a heterozygous SNP with short read, then phase it with long-read.
But in long-read, at the same position is not a heterozygous SNP,
may be it is a homozygous SNP or no SNP.
What wi…
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### Context
Related to https://github.com/nextstrain/auspice/issues/1549
### Description
`augur export v2` should allow users to define the gene order of the genotype color-by through the auspice…
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Hi, Lolita,
After running:
python3 SVJedi//svjedi.py -v $dir/Chr12.INS.CW01.seq.vcf -r nip -i reads.pass.fastq.gz -o $dir/Chr12.INS.CW01.gy -t 4 -d ont
I got this error:
Traceback (most recent c…
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In the context of somatic mutations there is no easy way to represent a genotype in the same way as in germline variants. For this reason, some somatic mutation callers, do not provide genotype inform…
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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…
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This was discovered when I wanted to download the genotyping files of all ppl that have entered the peanut butter preference (c.f. https://twitter.com/gedankenstuecke/status/943205612837486592).
Yo…
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It is a genotype rather than a gene.
From @pnrobinson
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## Problem
Match prediction is an intensive process.
It is also deterministic: same input will result in same output.
Thus caching calculations could save on computation.
Input for match prediction:
…
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Hi -
I've gotten the tool up and running and it seems to be working well. However, I am trying to understand how well my genotypes are defined/separated. How can I do so? I tried to recreate the c…
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I was looking for a few of these to fix, and they are tricky to locate in big sessions with lots of similar alleles.
I suggest a small link in the genotype panel (i.e like the one we plan to add t…