Since the genome build for this GWAS is labelled as HG19/GRCh37 (on OpenGWAS website https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST005071/), the SNP with GRCh38 position might actually be another SNP with a different rsid? Otherwise, its position is incorrect...?
This error is found after the GWAS data was clumped using tophits("ebi-a-GCST005071", clump = 1, pval = 0.05). So there might be other SNPs with the same issue in this GWAS.
Dear team,
Using the code: extract_outcome_data(snps = "rs2102259", outcomes = "ebi-a-GCST005071") of TwoSampleMR package in R, two variants with the same rsid but different position and effect allele were extracted from the GWAS. I think one of them is labelled with the position of rs2102259 based on GRCh38 (https://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=4:45979557-45980557;v=rs2102259;vdb=variation;vf=91509913), the other one is with the position based on GRCh37 (http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=4:45981574-45982574;v=rs2102259;vdb=variation;vf=306912102).
Since the genome build for this GWAS is labelled as HG19/GRCh37 (on OpenGWAS website https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST005071/), the SNP with GRCh38 position might actually be another SNP with a different rsid? Otherwise, its position is incorrect...?
This error is found after the GWAS data was clumped using tophits("ebi-a-GCST005071", clump = 1, pval = 0.05). So there might be other SNPs with the same issue in this GWAS.
Thanks in advance for looking into the issue!