Can genotype imputaion be done for multigeneration family study? While dealing with single multigeneration family with several affected individual of some genetic disorder and when the whole genome snp array data are available but want to impute all the flanking snps or wanna get a complete overview of the whole genome by imputing by means of gap filling between all the snps of the array probe.
When you say single family with several affected individuals from different generations, you should have sequenced the exome or the whole genome to study rare pathologic variants. SNP arrays target the common known variants, the knowledge of which will be of minimal or no use in your situation. Regarding imputation, imputation works fine for the common variants since their haplotypes are well known for different populations. Using the array SNP genotypes you can certainly impute the common variants using softwares such as Beagle, IMPUTE2 or MACH. But the resulting information will be of no use to study the family.
Thank you very much for all your comments and suggestions Veera. I do have whole exome seq data too for the same, along with that I have whole genome snp array data too. I have some diffrent hypothesis where I dnt want to look into the rare pathogenic variants only, the disease I am studying its a high prevalent disease with high penetrance. I am very much clear about my hypothesis and I have achieved my goal too.
All my confusion is regarding imputation. I wanna get a complete view of the whole genome where along with that I can cross check the exome seq finding too. But why did you say that " the resulting information will be no use to study the family"? actually here I got stuck. I have extensively tried to do imputation through plink, but not successfully able to do that and then when I extended my search and find that probably there are population data usually use to impute in PLINK and mine is family data. and as per I have know in BEAGLE and IMPUTE2 also works in near about same manner. So, whether for that reason, I am not getting to do, what I am seeking for?Or in family stuady its not able to do imputation? can you plz clarify once more why you said that there is no use in the family study. If its really like that then I will leave trying like hell.
From the Beagle documentation manual, "Beagle can perform haplotype phase inference and missing data imputation using data from unrelated individuals, parent-offspring trios, parent-offspring pairs, and phase-known haplotypes." So, Beagle can impute your samples. I guess yours should be either trio or parent offspring pairs. The reason for saying that the resulting information is of minimal or no use is because in order to study common variants you need a larger sample size. So the with single family, you cannot infer anything about the common variants.
