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Hi, i converted the UKB chr22 BGEN file to VCF format using PLINK2. I first used PLINK to run association analysis on these two input files to make sure that i got the exact same results.
Then I…
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- Patients on warfarin at enrollment and those that were put on during follow-up. Note that we only want to count warfarin/NOAC if they took medication before ischemic stroke event (not events that oc…
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Hi!
I am currently using the --ref-ld-chr-cts option to perform S-LDSC analysis, and I have a few questions:
1. The output of my analysis only includes the columns Name, Coefficient, Coefficient_s…
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Hi,
we have observed two problems with flashfm, using 4 traits with UK Biobank data, that we could not solve on our side.
Both stem from the makeSNPgroups2 function:
1. There are some regio…
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```
File "/anaconda3/envs/kipoi-gpu-shared__envs__kipoi-py3-keras2/lib/python3.6/site-packages/kipoi_veff/snv_predict.py", line 795, in score_variants
return_predictions=return_predictions)
…
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We plan to update gnomAD to v4, when available, and several updates will be needed.
Master list of tickets (in order of priority)
- [ ] #344
- [ ] #345
* includes updating the group table…
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Dear David:
Please refer to my post at PLINK users group:
https://groups.google.com/g/plink2-users/c/Xvt895jb48w
It seems that **there is no readl ChrY data from the UK Biobank genotype datas…
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I got "After merging with reference panel LD, 0 SNPs remain." for my MTAG analysis.
I found [a previous issue](https://github.com/omeed-maghzian/mtag/issues/8) discussing similar warning.
But my …
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Currently `ldshrink` assumes the input genotype/haplotype data are stored in an [n-by-p numerical matrix](https://github.com/stephenslab/ldshrink/blob/901d911677c858590ae88374fe3323535a60550a/R/LDshri…
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When using a linux serve(4 core & 8G) to run this job on the example data you suggest, I can' t get the result after around 5-6 hours cost. And the snakemake log shows the info as below:
Could yo…