I've done SNP (6000 SNPs) genotyping of 220 plant varieties using illumina platform, but the file contains a lot of missing values and I want to impute to get them filled. But I do not have any reference panel for this purpose which is most commonly required in human SNP imputation. Can I do SNP imputation without reference panel. Can anyone help me in this regards. Thanks
Illumina Infinium custom arrays was used for genotyping of 6000 snp for 220 individuals. SNP data were analyzed using GenomeStudio V2010.1. SNP genotypes were called using genotyping (GT) module integrated in the software where individual SNPs is viewed as GenoPlots. Data quality is rapidly confirmed with internal controls and other QC functions such as GenTrain and GenCall scores. After calling the data automatically, the SNPs were re-scored and manually adjusted in a canonical cluster to get a GenTrain score >0.7. Finally we removed any samples from the analysis that had call rates <0.2, as we suspected these samples may be prone to error at those loci for which they were called. SNPs, genotyped for a single type of allele and with low call rate were removed from the dataset. I am talking about theses SNPs which were removed because of low call rate and which were not custered. And theses SNPs in the final ped file is written as missing genotypes, they hybridized but not achieved the critical level of success. So, some software is there to impute theses missing values but in human a reference panel is always required to fill these missing values.