Merging SNPs from multiple imputation runs
Hi,
I have imputed genotypes surrounding a number of genes using IMPUTE2. Some of these genomic regions overlap so that I end up imputing a given SNP multiple times. Is there a nice and easy way to merge these files into a single one (preferably vcf format)? In particular, I want to merge genotype if the imputations agreed and somehow mark genotype if the imputations disagreed. Is that possible?
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