The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
New representation in VCF (Genotype GVCF bug fix from v3.4) and downstream annotation
I am using GATK3.5 and I can see the new IUB <*:DEL> representation to accomodate the SNPs in the spanning deletions in a region. But this hinders the downstream annotation. Do you guys recommend a specific annotator that takes this new representation into consideration?