Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
AF in vcf files
There is some inconsistency in the community on how to calculate the AF (allele frequency) value in vcf files. GATK calculates a hypothetical value (0, 0.5 or 1 for normal diploid organisms). Other callers will calculate the AF as an Alt Allele Frequency.
Is there a way to have both values in the VCF file from GATK?