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Which is the best tool for Variant calling of a non-model organism (Non-tumour)?

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Hi All.

I have been using #Haplotyplecaller for SNP calling for my organism of study. Recently, I came across #MUTECHT2 tool by GATK which states that it works better for calling spmatic mutations. But my doubt is does it work for Non-tumour samples, If YES then would it be beneficial to switch to MUTECHT2 from Haplotypecaller?
@Geraldine_VdAuwera @Sheila

Best,
Jigar


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