FSFHap to ABH format

[Isabel Werle]

I used FSFHap for genotype imputation and need to convert the sites coded as A (parent 1), C (parent 2), or M (heterozygous) to ABH format to run in the r/qtl package. Is there a way to do this in TASSEL? I cannot use GenosToABHPlugin because the parent genotypes are not available.

Thanks,

Isabel

[Hugo Cuevas]

Linkage map construction using limited parental genotypic information | Euphytica

https://link.springer.com/article/10.1007/s10681-022-03005-z

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[Peter Bradbury]

No. There is not a tool in TASSEL to make that conversion. You will either need to do that yourself converting A -> A, C ->B, and M->H. Alternatively, add genotypes for the parents to the imputed genotypes, where one parent is all A and the other parent is all C then use the GenoToABHPlugin.

Peter