Merging biological replicated SNP data to create a consensus SNP data for a sample

Question

[AF]

Hello everyone,

I have obtained SNP data from three biological replications of two different plant varieties, parent1 and parent2, which are involved in a genetic mapping cross. Each parent was replicated three times. Now, I am looking for a suitable software or command tool to generate consensus SNP data for parent1 and parent2 based on their respective biological replications. This consensus SNP data will be used for creating linkage map. Any suggestions or recommendations on software or command tools for this purpose would be highly appreciated.