Find causal mutation for a special trait in one population

Question

[dominik.lagler]

Hello,

I wanted to ask the lovely world, how would you call a SNP or SV when you have 50 bam files from 50 different animals. 25 of them have blue eyes and 25 of them have brown eyes and you would like to find out what is the causal mutation for brown eyes. You allready know the mutation is on chr11 Region 36,600,000-37,900,000. Squencing data achieved from Capture sequencing. Thank you very much for your advices