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**THIS ISSUE IS NOW OBSOLETE. PLEASE SEE ISSUE #52 INSTEAD.**
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Hello,
I am trying to use SHAPEIT4 for phasing a large cohort (~2,000 samples) of whole genome sequencing data and I'm runn…
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Hello! Thanks for making this open-source and for putting together such an informative README. I'm still wrapping my brain around branching and the pedigree def file, but for now, I'm using your examp…
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This issue is primarily about pulling required documentation together for this issue in one place.
## Goal
To perform filtering through variant quality score recalibration to ensure high quality v…
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- `sgkit` cost estimate on UKB data: https://github.com/related-sciences/ukb-gwas-pipeline-nealelab/issues/32
- `hail` cost estimate on UKB data: https://github.com/Nealelab/UK_Biobank_GWAS/issues/37…
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Hi
I am trying to fit some protein AA variant data into the model and Baylors documents. I can make a protein simple allele document from our data but I am not certain I can always give the correct A…
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I got these warnings:
```json
{
"schemaValidationMessages": [
{
"level": "warning",
"domain": "validation",
"keyword": "format",
"message": "format attribute \"ur…
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When running GENESIS v. 2.13.11 and supplying an interactive term for the score test, I get the following error after all iterations are completed:
> Error in match.names(clabs, names(xi)) :
> …
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Hi Yoav,
I hope you had a good Easter break. I have a question regarding choosing the K-mer location based on read alignments from Bowtie2 as you did in the paper. For example, I have 10 K-mers for w…
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Hi Florian,
Firstly, this is a great package and I am excited to use it. I came across the following error while using snp_match()
10,707,059 variants to be matched.
20,946 ambiguous SNPs have b…