SNP calling for parentage verification in non-model organism

henriettevdzhenriettevdz South Africa Member

Hi! My project entails de novo sequencing and assemblying of an offspring lovebird and then resequencing the parents. The assembies are done and we want to use the offspring as the reference genome and map it against the parent's genomes in order to identify SNPs that can be used for parentage verification. Which tool will be best suited for this application? Will Mutect2 work well or can you recommend a better tool?

Thanks!
Henriette

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