Finding functional variations from resequenced (WGRS) data

Question

[Bioin]

Dear Biostars,

I have two contigs (expected marker locus) obtained from two different parents forward and reverse amplicons of respective parent. My objectives are: 1. to find out the locus and associated genes from each parent's resequenced (WGRS) data. 2. Functional annotation of genes. 3. Calling variations, comparing variations between locus associated genes of different parents. 4. to find out functional variations.

I have reference sequence, and consensus sequence constructed on reference based assembly of two parents resequenced genome. I request your inputs about strategies and best tools to solve above objectives.

Thanks in advance