How to find mutations occuring in homozygoud region?

Question

[Tori]

I have an Adabidopsis offspring obtained by crossing Col-0 (Columbia) and Ler-0 (Landsberg erecta). I am interested in mutation occurred in homozygous region of Col-0.

I have mapped the sample to both Col-0 reference genome and Ler-0 reference gemnomes separatley and called variants separately using GATK. I have variants in vcf files.

I am not totally lost how can I get the mutation occurred in homozygous region of Col-0.