Tools for SNP imputation
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10 months ago

Hello,

I am working with polyploid plant species (tetraploid, hexaploid, octaploid). I have genotype by sequencing (GBS) SNP data from different sequencing platforms like Affymetrix and SeqSNP. Now, I want to perform SNP imputation for some species and increase the number of SNPs and also find overlapping SNPs from two different sequencing platforms. I do not have Map information but I do have a reference SNP dataset. I see that there are lots of tools like Beagle, Impute etc. to impute SNPs. But these tools are specifically used for diploid organisms.

Since I am working with polyploids, can anyone suggest me some tools for SNP imputation in polyploids?

Thank you

SNP Genotyping imputation • 646 views
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What about https://academic.oup.com/nar/article/49/D1/D1480/5952206 and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404598/

Plant genomics is hard and I think fairly niche (unfortunately). I dont know many plant bioinformaticians.

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Thanks a lot for the suggestions. The first one only has 12 plant species and none of them are my use, unfortunately. The second one is interesting. But still not enough.

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