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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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I am getting same result using "MLM","CMLM", "MLMM","Enriched CMLM" model. In GAPIT there are total 10 models. Is there any scenario, when the above mentioned models give same result in GWAS.
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We run the gwas based on our WGS dataset ,so no imputation ,no INFO value. So is there no need to run the Quality Control of GWAS summary statistics?
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I am running a GWAS on 94 Ornithobacterium rhinotracheale isolates using the gene presence/absence matrix generated by panaroo as input, a phenotypic binary vector for each antibiotic (1 = resistant o…
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Is there any instruction and information for how to run the bivariate model for gsa-mixer using fit2 and test2 functions and inputting two GWAS (trait1.sumstats.gz and trait2.sumstats.gz)? Can you pro…
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Hi,
We are thinking about applying mashr for gwas studies. The gwas studies contain same samples of single phenotype at different time point, or multiple related phenotypes.
Because gwas contains…
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We need to find a good dataset for testing the implementation of the pipeline.
This issue stems from a discussion documented here https://github.com/nf-core/gwas/issues/16#issuecomment-1030649162
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Hi, guys:
We could use bcftools to merge multiple regular VCF files with genotype data.
Now, I have multiple GWAS VCF files, each of which have rsID, REF, ALT, BETA, SE, P, etc.
Can I use bcf…
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This was a major request at the May 5 AMP meeting. Users wanted to search for variants that are significant in multiple traits.