I am currently working on rare variants association studies from whole genome seq data. I want to replicate my results in an array-genotyped cohort where rare variants have been previously imputed with Michigan imputation server based on Haplotype Reference Consortium panel. However, I found out that my top hits have been badly imputed and therefore I would like to re-impute rare variants based on a custom reference panel built on my own wgs data. I see that IMPUTE2 and SHAPEIT are widely suggested to this purpose. However I can't find any clear explanation about how to generate a reference panel. I have individuals vcf files and plink files and also a merged plink ped file including all the samples.
Could anybody kindly suggest me any tutorial/resource where I can learn how to do it? Is there another better strategy to impute those rare variants missed by Michigan server rather than generating my own reference panel?
Thank in advance for any help.