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Frontmost snp callers for plant genomes

Hello! I'm working with WGS data and looking for the most used software to find high quality SNPs and INDELs in plants with different ploidy levels. I've found two related posts, but seems they both already not up to date and futhermore not focused on plant genomes:

A: Snp Calling Tools And Costs
Variant Caller Of Choice?

Could you help me please?

alignment next-gen snp genome

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1 answer

For plants and other polyploid organism I prefer FreeBayes

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