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How to get a smaller list of deNovo SNPs between 3 genotype

Hello. I am currently working on maize whole genome dataset and I have 3 samples- WT, MT and B73. I obtained the VCF files for all 3 datasets using the haplotype caller. However, the list of SNPs that I am getting on comparing these 3 samples on just chromosome 3 is more than 200,000. Is there any way, I can get a shorter and more complied list of de Novo SNPs which I could possibly work on?
I also had another question related to creating the .ped file for my 3 samples of maize. Is there anyway that I can create a .ped file for maize samples as I want to do a trio analysis on the same samples and what are the tools that I can use to create this file. Thank you.

Answers

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