How to impute missing SNPs of genotypic data of plant species, without having HapMap reference panel?
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6 months ago
Abbas.M • 0

hello all, I have a SNP genotype data of 228 accessions of cotton, on which I want to do GWAS. The genotype data has a lot of missing SNPs, which should be imputed. I have calculated genotyping rate in plink, which is 0.72. My goal is to do GWAS. The genotype data is already published, and I downloaded it from a link given in the supplementary portion of the paper. They imputed it from beagle, but when I tried to contact them, they didn't answer me. The format of genotypic data they published, does not follow any format, neither vcf nor hapmap or any other format. I converted it in hapmap format manually for association in GAPIT and TASSEL. But Beagle does not support hapmap, so I converted in VCF format with TASSEL, which also looks like wrong. To impute the missing data, I run imputation in beagle, and got the results. But as far as I read in the literature, a reference panel is used for imputation. But in the case some crops, where there is no any reference panel. What to do? I run the imputation without any reference panel, and I am not sure, whether my imputed results are right or wrong. Need suggestions.

snp SNP genome R • 424 views
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4 months ago
SiegmundWANG ▴ 10

Why not try STITCH? "Rapid genotype imputation from sequence without reference panels".

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STITCH is great, but requires the read sequencing data in BAM or CRAM, sounds like the OP has just the called genotypes?

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