We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

New representation in VCF (Genotype GVCF bug fix from v3.4) and downstream annotation

ravichavravichav United StatesMember
edited January 2016 in Ask the GATK team


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?

Best Answer


Sign In or Register to comment.