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Problem with annotating GATK4 VCF file
Based on GATK4 best practices pipline I have made a VCF file composed 4 person WES data. When I want to annotate it with annovar , but annovar could not annotate all variations and near 70% of variations discard and gone to Invalid_input.
I though it might happen due to VCF version (4.2), but it doesn't work with annovar default input format (avinput).
What is your suggestion for annotating GATK4 output VCFs?