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.
Allele Balance for ABHets & ABHom
Is there a threshold value for the annotation ‘Allele Balance’ to call the SNP as heterozygous or homozygous call? I have calls where ABHet=0.073 and ABHom=0.100; it would have been more appropriate to call the former an alternate homozygous call and the latter as homozygous with the reference and not called at all by UG.