To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

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?


Sign In or Register to comment.