LinkImputeR is a Java tool to call and impute genotypes. The LinkImputeR algorithm uses the read count information and all other available sequence information. LinkImputeR works particularly in non-model organisms because it does not need genotype reference panels or ordered markers.
Money D, Migicovsky Z, Gardner K, Myles S "LinkImputeR: user-guided genotype calling and imputation for non-model organisms." BMC Genomics. 2017 Jul 10;18(1):523. https://doi.org/10.1186/s12864-017-3873-5
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