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Now that we have a rudimentary [Genome](https://github.com/Terasology/genome) module more or less in place, we should start working on integrating Genome into SimpleFarming.
A high-level descriptio…
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> Advanced machine learning models applied to large-scale genomics datasets hold the promise to be major drivers for genome science. Once trained, such models can serve as a tool to probe the relation…
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Hello
I am somewhat confused by the output by `geneitc_diff()`, in particular the number of alleles in each population.
Given the example data below:
```
library(vcfR)
data(vcfR_example)
…
EveTC updated
3 years ago
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I'm trying to phase a vcf with 983 exome samples.
The command I ran -
```
/mnt/exome/Softwares/shapeit4/bin/shapeit4.2 --input MOD_hg19.vcf.gz --map /mnt/exome/Softwares/shapeit4/maps/chr"$chr"…
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We initially defined the variantOriginQualifier as refining the statement/annotated knowledge to indicate that it hold for variants of a particular genetic origin (e.g. germline vs. somatic).
It h…
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We should start thinking about how to simulate data as part of a public API. PLINK and Hail support this and I think we should think about it now because it will be an important part of improving uni…
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Hello, I'm getting a cryptic error that I believe is related to reading the groupFile. The groupFile is properly formatted, so I don't know who could be causing the typing error.
Here are the most r…
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Hello,
I have HiSeq data from some yeast experimental populations and I would like to compare population parameters between populations (samples). For example, I would like to estimate genetic divers…
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I'm thinking about trying this out for a backend for my VEBA eukaryotic binning module (https://github.com/jolespin/veba) as an alternative to MetaEuk.
Looking at the examples here:
```
Helixer.…
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Documentation on the fastsmc map file (https://github.com/PalamaraLab/ASMC/blob/main/docs/fastsmc.md#genetic-map-map) are unclear:
> The genetic map file needs to provide physical positions (in bas…