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1000FARMS.climmob needs a consistent well document list of varieties/genotypes aligned with BMS https://bmspro.io
Also when the list becomes too long we need to develop an approach to select genot…
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A typical genotype entry looks like:
`0/0:43,0:43:92:0,92,1267`
The first part `0/0` is the actual genotype; the others are genotype annotations. In our current implementation (vat 2.0 hereafter…
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(part of #383)
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#### Introduction
Testing of the prototype showed that it met the MVP requirements of #383.
Testing also suggested a number of usability enhancements which could be made to impr…
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### Description of the issue:
When reading a VCF with HTSJDK it causes an exception when there is a duplicate ALT allele.
I believe duplicate ALT alleles are allowed in VCF, and are used in cases wh…
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for some genotype calls the pagination should be changed to match BrAPI v2
these switched from currentPage to currentPageToken and nextPage to nextPageToken
Calls
CallSets
Variants
VariantSets
…
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HiFiCNV currently outputs `0/1` as a placeholder GT value for all cases. Set policy to either make this unknown or provide a consistent interpretation of copy number as GT.
ctsa updated
9 months ago
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Cell attaches a data structure called `Genotype` to each node to allow each node to manage its own state in a decentralized manner.
So if you take any node created by Cell, and query its `Genotype`…
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### To Do List:
- [x] filter the fam file for only eur based on the file of `EUGEI_GROUP_EuroOnly_PCs_NonRefPanel_Dec17.txt`
- [ ] only 794 left
- [ ] the third column of the bim file (Position i…
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Hi, how do I retrieve the genotype column ID for `genotype[x].compute()["probs"]`?
Hoeze updated
5 years ago
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Hi, I meet the error below when I was running whatshap genotype.
```
======== Writing VCF
Traceback (most recent call last):
File "/home/zicong_zhang/miniconda3/envs/whatshap/bin/whatshap", li…