Hi. I would like to colocalize a number of regions that I have identified through a gwas (not yet published), with a number of opengwas datasets.
As I understand, I first need to convert my summary statistics (b37) into a dataframe, and then create a vcf (https://mrcieu.github.io/gwasvcf/articles/guide.html#creating-the-vcf-object-from-a-data-frame-1).
Then, I should harmonise this vcf, before doing any colocalisation (https://mrcieu.github.io/gwasglue/articles/gwas2020.html#all-data-is-now-harmonised-1: "alleles are coded on the forward strand, and the non-effect allele is always aligned to the human genome reference sequence B37 (so the effect allele is the non-reference allele)").
Could you kindly tell me if there is a pipeline or script that I can use to perform the harmonisation of my sum stats in the same way as the opengwas vcf's were harmonised?
Thank you so much!
Matteo
Hi. I would like to colocalize a number of regions that I have identified through a gwas (not yet published), with a number of opengwas datasets. As I understand, I first need to convert my summary statistics (b37) into a dataframe, and then create a vcf (https://mrcieu.github.io/gwasvcf/articles/guide.html#creating-the-vcf-object-from-a-data-frame-1). Then, I should harmonise this vcf, before doing any colocalisation (https://mrcieu.github.io/gwasglue/articles/gwas2020.html#all-data-is-now-harmonised-1: "alleles are coded on the forward strand, and the non-effect allele is always aligned to the human genome reference sequence B37 (so the effect allele is the non-reference allele)"). Could you kindly tell me if there is a pipeline or script that I can use to perform the harmonisation of my sum stats in the same way as the opengwas vcf's were harmonised? Thank you so much! Matteo