PxSNP v1.0

VÝZKUMNÝ ÚSTAV ŽIVOČIŠNÉ VÝROBY, v.v.i. V UHŘÍNĚVSI. PxSNP v1.0. Authors: KLÍMOVÁ, Anita and KLÍMA, Jakub.. Česká republika. Software PxSNP. 2020-11-10.
CathegoryMethodologies and software
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The PxSNP program is used for the editing of raw genomic data. The program includes the control of input data for the applicability of various formats for further processing and the preparation of genomic data for imputation in the FImpute software (Sargolzaei et al. 2014). The program also includes a simulation package SIMPUT, which is used to verify the accuracy of imputation depending on the size of the reference population and the number of missing SNPs. One of the parts of the PxSNP program is focused on pedigree control and detection of cycles that often occur in pedigrees. The PxSNP program is able to prepare raw data for imputation and then modify it for further use using reverse conversion. The reverse conversion changes the data to the original form or the form of an input file for the prediction of breeding values in the BLUPf90 program (Mizstal et al. 2018).