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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

Hello,

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?

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