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Hello,
From your documentation, I see that HLM is used in the GxE testing framework. I was wondering whether it is possible to estimate variance effects at SNPs without including an environmental cov…
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Hi,
How to use MTMM normaly if one without ASREML-R?
Best,
Kun
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@david4096 provided an [example](https://gist.github.com/david4096/9dcba9b8b25ba3cec6a104a6e124b08a) from interchange of the `Populations` field of
the 1kgenomes data:
```
"Populati…
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Hi!
I'm trying to implement PolyGraph, but I got the issue from running the MCMC part.
Right now, I use the dog GWAS dataset, and I got the admix graph using admixtool2, then converted it to the 'a…
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While running "sos run GWAS_QC.ipynb king --cwd output/ --genoFile ZOD14598_AD_GRM_WGS_2021-04-29_chr20.recalibrated_variants.leftnorm.filtered.bed --name test --keep-samples sampleSheetAfterQC.filter…
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Summary of MTAG results:
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Trait # SNPs used N (max) N (mean) GWAS mean chi^2 MTAG mean chi^2 GWAS equiv. (max) N
1 ...peline/QC/trait1.txt 5820480 …
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I applied switch error rate checking on all ~7000 trios in ~/meta/trios_for_bcftools_mendelian.ped in ~/data/phasing_test/shapeit4_full_all_snp_wrong/
1. directely on gwas.phased.vcf.gz
2. only 100 …
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The paper goes back and forth on the use of various abbreviations. The following abbreviations should be checked that they are (1) defined at first use, and (2) always named via abbreviation afterward…
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Hello,
I was running pwas for my own dataset, without providing a covariate file for the test run, and I have trouble solving it myself.
I ran into this error, I wonder if it's because I didn't …
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