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how to get known variant VCF file to recalibrate human mitochondrial NGS data with GATK4

laki5laki5 SRILANKAMember
Im analysing human mitochondrial NGS sequences for germline variants. Im using GATK4 and wondering if recalibration is necessary, and whether base recalibration and variant recalibration done in a single step. and if so, how should I get known variant VCF of human mitochondrial DNA ; is there a way to do it if I dont have that file?

Also curious what should be done about the realignment step as that function is deprecated in GATK4


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