I have a query about imputing specific SNPs in genotyping data. I have a small dataset in Plink format, which is missing certain SNPs that I want, i.e. rs1234. I would like to impute these and have been pre-phasing my data using ShapeIt. It only pre-phases by chromosome and then imputation using impute2 is performed for chunks of the chromosome.
However, I would like to merge these imputed regions with my original plink data files - is this possible if the rest of the regions are not imputed?
E.g. 1) My original dataset is plink.bed plink.bim plink.fam
2) I extract chromosome 1 and pre-phase with ShapeIt
3) Then impute the region chr1:1-5000000 as my SNP rs1234 is at position 10. This will result in snp1234_imputed.gens file
How would I merge the resulting imputed file with the original plink dataset? Is it possible or would I have to impute the whole genome before I can use it?
I'm quite confused, so sorry if this makes no sense. Thanks in advance any help is appreciated!!
