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Hi,
I am running a big simulation with a million people and I'd like to calculate the genealogical relatedness between them. I tried running sgkit and unfortunately, when I hit the ped.compute() st…
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Could we make the pedQa functions work without assuming that we will have access to the original genotype file? Assuming this will not be a realistic scenario when deploying in the servers where files…
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From Veronica's todo document:
> • Add total individuals to ped ascertainment summary view, and sort by # affecteds
> o Confirm people outside the cohort are included
> o Confirm total individual…
Viqsi updated
1 month ago
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Hi
I'm trying to do some imputation checks by masking the genotype data and it worked well with the original file but always get errors when I use the file that I added random 9(missing value) into t…
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What happens if we have intentional proband duplicates? Is there a way to specify relatedness=1, or duplicates in the pedigree files?
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HI
I am trying to draw a large pedigree but by even limiting the pedigree to only breeding pairs I am struggling.
I have tried different import orders but nothing changes. Do you have any advice…
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[VCF 4.3](https://samtools.github.io/hts-specs/VCFv4.3.pdf) allows pedigree data to be stored in a VCF header. This could be translated to the `parent_id` variable.
I haven't actually come across t…
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Was: [GitLab #47](https://git.lumc.nl/nested/nested-editor/issues/47)
We need a unique id for pedigree document so that we can detect loading/opening a new document in the editor. This property will …
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- whatshap (v2.2), python (v3.10)
- conda create -n DEEMPRINT_whatshap whatshap
----------------------------------------------------------------------------
```
rule wh_phase:
conda:
…
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Greetings,
I have peculiar situation on my side with FamAgg.
The Pedigree I use is quite convoluted as it come from breeding company data.
If I use a "complete" pedigree, several birds are dupl…