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hi, I might have a rather basic question. PRScsx is a great tool, and I believe that if I use one GWAS data from EUR population along with 1000G reference genotypes, and my target bim file is from the…
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Hi @freeseek ,
Thanks a lot for the tools provided in this repo.
I have a question with regard to the munging plugin, it appears that indel variants are systematically flagged when the alleles are …
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Hi,
I encountered this issue when I tried to use ldpred coord using 1kg EUR as reference. I tried LDpred v. 1.0.8, 1.0.11 and the develop version and all threw the same error message.
the fallowing …
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We convert the UKB sumstats into LDSC munge format.
This will enable us to perform
- GBE global meta-analysis #25
- Compute LDSC intercept as a GWAS QC metric #21
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Hi,
Is `TwoSampleMR` solely based on dbSNP-style rsID, or would it also work with IDs styled based on chromosome base pair positions, _e.g._ 1:23467230?
The latter would make the tool more flex…
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Could you please tell me how Alzheimer's disease GWAS data file ieu-b-2.vcf.gz results in maf and beta, or can I get these reproduced input data?
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Hi,I am running mtag using 1trait, i met the following issue:
Trait 1: Dropped 1971 SNPs for duplicate values in the "snp_name" column
Dropped 920120 SNPs due to strand ambiguity, 4996132 SNPs remai…
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I'm running mtCOJO using following script and getting nan values for bC , bC_se, bC_pval in the mtCOJO results.
The run has successfully completed but much helpful info in the log.
Can you pleas…
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Hi @joellembatchou ,
Along with this issue https://github.com/rgcgithub/regenie/issues/256 and the other here: https://github.com/rgcgithub/regenie/issues/454
I have a similar question: If we spe…
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Hi ,
I am trying to convert summary statistics using ./mtag_munge.py command but it is throwing me the error.
ERROR converting summary statistics:
2022/09/25 10:34:09 AM Traceback (most recent…
ghost updated
2 years ago