Funcotator does not always annotate multiallelic VCF records with both an insertion and deletion correctly
open | Created 2018-10-29 | Last updated 2018-10-29| Posted by droazen | See in Github

Funcotator bug

With multiallelic VCF records such as Ref = ATA, Alt = A,ATAAT we don't always annotate correctly. In particular, we often use the length of the reference allele to compute overlaps. If the insertion were in a record by itself, the ref allele length would be 1, but in multiallelic records with a deletion it can be > 1. This can lead to "false positive" overlaps for insertions in multiallelic records (for example, we might falsely conclude that the insertion overlaps the UTR).

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