The frontline support team will be slow on the forum because we are occupied with a GATK Workshop on March 26th and 27th 2019. We will be back and available to answer questions on the forum on March 28th 2019.
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?