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This is my command:
!python /Users/halk/MetaXcan/software/SPrediXcan.py \ --model_db_path /Users/halk/Downloads/eqtl/mashr/mashr_Whole_Blood.db \ --covariance /Users/halk/Downloads/eqtl/mashr/mas…
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As a **community user** I want **to be able to understand how the Gentropy ariflow pipeline works ** because **I want to reproduce it with nextlfow.**
## Background
Background to this task is a…
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Hi,
I tried to convert my GWAS data into a sumstats file using munge_sumstats.py.
When you look at [https://github.com/bulik/ldsc/wiki/Summary-Statistics-File-Format#sumstats](url) , it says tha…
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Dear Team,
I calculated partition heritability for ATAC seq peaks by using 106 GWAS sumstats.
For example: for "PASS.Schizophrenia.Trubetskoy2022 GWAS sumstats", I have 98 categories for peaks. I …
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Hi,
The two-stage imputation strategy is great. Thank you for the method!
I have tried tsim in two differently genotyped independent Cohorts after the first imputation using the same reference panel…
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Please note - details below are going to be discussed in person next week.
See [here](https://genetics.opentargets.org/study/GCST002222) for current Open Targets Genetics study page.
- [ ] Scenari…
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This submission '665086c4d222f500010e2aba' was pushed through validation due to one file being non-standard ('GCST90429842').
This should mean all the meta yamls (44 studies) are given file_type 'no…
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The current file type for these 2 studies is GWAS-SSF, as the user has populated the beta and SE columns with values '0', and the z-score column is provided after the p-value column. The file type sho…
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Hi! Thanks for the great approach! I have two GWAS summary datasets and I want to do co-localization analysis on these two GWAS datasets using significant SNPs. Can echolocatoR achieve this goal?
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When I try to run mtcojo, the following error is reported, but when I check my data, there are no duplicates of SNPs, and I don't know what the reason is.
**Accepted options:
--mbfile test.txt
--…