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Hello,
I'm using Regenie v3.2.9
I run the low variance plink fix after getting the error running Step 1:
`plink2 \
--bfile subjects_sex \
--chr 1-23 \
--mac 100 \
--write-snplist \
…
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As reported in a recent [community post](https://community.opentargets.org/t/duplicated-diseases-in-22-06/702/2), some diseases that used to have `disease2phenotype` relationships ([ETL code](https://…
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Hello,
It has been a while now that I am using this powerful tool which is tensorqtl so thanks for the work. Recently, I'have tried to perform a cis-mapping with an interaction term (which is the s…
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Hi, I am trying to run GEM analysis, but it keeps showing an error about phenotype file. I have attached my code here. Do you know what is my problem here?
singularity exec \
> -B /humgen/ManningL…
lc491 updated
6 months ago
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## Dataset PID
Propose
`urn:fdc:australiangenomics.org.au:2022:dataset/acute-care`
- [ ] agreed PID
## Data model
Is meant to be 280 trios.
- [ ] agreed data model
- [ ] able to imp…
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Hi Doug,
I am running into an error when LDAK is reading in the covariates file. I've tried changing the file from tab to space separated, removing any non-alphanumeric values from the variable nam…
sahwa updated
1 month ago
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## Dataset PID
`urn:fdc:australiangenomics.org.au:2022:dataset/cardiac`
- [x] agreed PID
## Data model
Cases consist of individuals except for some limited trios? Case ids are ???
Individ…
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Hi, We ran the gene burden test with the following command and found that some variants that were included in all the input files got excluded from the built mask (the .snplist output) or the final .R…
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Dear REGENIE developers,
I'm using REGENIE v3.5.gz on 237 cases and 387 controls. Genotypes of my samples were jointly called from WGS data, which had 50,811,891 variants. It was mentioned that 44…
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[root@181-12-19-171 examples]# ../bin/SuSiEx --sst_file=EUR.sumstats.txt,AFR.sumstats.txt --n_gwas=50000,50000 --ref_file=EUR,AFR --ld_file=EUR,AFR --out_dir=./ --out_name=SuSiEx.EUR.AFR.output.cs95 -…