I am doing Genome Wide Association Study for Indian population. So far, study went well but now stuck with imputation. For this I have following two queries:
1) Since there is no standard Indian reference file, can I use 1000 genome Phase I V3 reference for my imputation in Indian population?
2) What does mean by following files? I mean, where will I get following mentioned files?
--snps chr.snps ----- SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel.
--haps chr.haps.gz ----- Phased haplotypes where missing genotypes will be imputed.
For any help, thanks in advance.