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Dear all,
I am evaluating possibilities for genotyping hundreds of fungal genomes and came across the Maast paper. Would you see any particular problem in applying Maast to fungal or eukaryotic gen…
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From a biological standpoint, the computational bottleneck highlights the challenge of dealing with vast amounts of genetic data to predict complex traits.
Section 2.1 of [this paper](https://www.nc…
hrluo updated
2 months ago
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It's pretty helpful for teaching purposes to be able to demonstrate small _tsinfer_ input files without needing a VCF. I wonder if we could define a class method like this:
```python
class SgkitSa…
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Dear Sirs,
I am trying to make HLA Genotyping for HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DRB2 and HLA-DQA1. Please tell me where can I find the HLA reference files in VCF format, as it is required for …
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when i run LDpred2 with gwas of biobank Japan for parkinson disease and target genotypes data is 504 samples of EAS in 1KGP, it raise an error: ldsc h2 estimate value is negative (h2 = -0.000936). I d…
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Hi,
I'm trying to use `gtfilter` (or `Filter GT`) module to set individual genotype calls to missing (`"."`) if they match a certain criteria.
I managed to do so when filtering based on a minimum de…
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HI,
In STRs we also have regions which will have interruptions in them, will HipSTR be able to genotype imperfect repeat regions if given in the .bed file or will it only genotypes perfect repeats…
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GQ, AD, MQ calldata were recently moved. The following code is apparently relying on out-of-date Zarr metadata and breaks when that Zarr metadata is updated.
```
# Set up call arrays.
calls_root …
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Increase parallelization by splitting the chr before joint-genotyping. Also prevents wasted effort genotyping chaff.