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Dear Wei,
Happy New Year!! Do we have best recommendation for GRM generation, for example, minMAFforGRM , numRandomMarkerforSparseKin, relatednessCutoff
Thanks.
Shicheng
createSparseGRM(…
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**Summary**
Tasks to follow up on email Subject: "Re: Plan to decomisioning last of the PSD tin and VM's", on Tuesday, 1 September 2020 at 14:16.
Following the agreed 4 step plan:
1. Decommis…
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Since the last time when UKBB GWAS studies were mapped to EFO, the ontology has suffered significant changes. The most notable the dynamic imports of some other ontologies (MONDO, HP, etc.). Due to th…
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Hi,
Is there any specific reason why `create_finemapper_jobs.py` creates overlapping regions in `--jobs-file` ?
For instance, `head -2 polyfun_all_jobs.txt`
```
python3 finemapper.py --chr 22 -…
Ojami updated
2 years ago
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### What you did:
We want to use the ancestry classification tool to predict genetic ancestry of UKBB samples. (https://gnomad.broadinstitute.org/news/2021-09-using-the-gnomad-ancestry-principal-co…
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Hi Joelle,
I was comparing the results from gene-based tests in step 2 (no `pred` file) to SKAT R package for different binary/quantitative traits using a single gene with the same number of varian…
Ojami updated
2 years ago
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Hi,
Thanks for updating REGENIE again - we've really appreciated the software you've made available in our department.
I've found that when running any SKAT/ACAT test, I get the following error:…
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Hi Tian,
Hope you enjoyed the holidays. I am having this error when trying to run PRScs on `iter-900`:
```
/project/ritchie/tools/PRScs/mcmc_gtb.py:55: RuntimeWarning: divide by zero encountere…
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Hello,
I am using UK biobank 500k imputed data for a gene-based analysis. for traits with sample size > 340k (quantitative traits) or 230k (binary traits) I get below error:
*** caught segfault *…
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Hi there, I'd like to ask if the use of snp_PRS() is compatible with BGEN file input? And if so, is the dosage data hard-coded?
Thanks