Imputing SNP information - SNP chip

Question

[chloe.p.oconnell]

Hi,

I have genotype information for ~680 SNPs in each of my subjects across the genome. For each subject, there are one or two SNPs that are not genotyped. Given that I don't have any read information or any additional information on the genotypes of these SNPs in these subjects, what is the best way for me to impute this data?

My current data is just SNP ID, along with a 0, 1, or 2 for each subject based on whether the subject is homozygous reference, heterozygous, or homozygous alternate.

I looked at Impute2 but it seems like this was designed to only impute a small section of the genome at a time. I don't care about imputing the entire genotype, just any of the missing 680 SNPs of interest in the subjects in which a SNP is missing.

[zx8754]

Look into -pgs, -pgs_miss, -fill_holes options, https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#options