Do I Need to Filter Indels Before Annotation in GATK Funcotator?

Question

[George]

Hi everyone,

I have a question about using GATK Funcotator. Do I need to filter indels before running annotation? I’ve noticed some warnings when processing indels, but I don’t believe they should cause any significant issues. However, I’d appreciate any insights or recommendations on this.

Thanks!

[Pierre Lindenbaum]

I’ve noticed some warnings

why don't you show us those warnings ?

[George]

I didn't include them because they re probably unrelated and my main question is if Funcotator can handle INDELS. Example of Warnings:

14:56:06.986 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 1 (size=1348, ref allele: G)
14:56:06.987 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 1 (size=1348, alt allele: A)
14:56:21.078 WARN  GencodeFuncotationFactory - Attempted to process transcript information for transcript WITHOUT sequence data.  Ignoring sequence information for Gencode Transcript ID>
14:56:21.227 WARN  GencodeFuncotationFactory - Attempted to process transcript information for transcript WITHOUT sequence data.  Ignoring sequence information for Gencode Transcript ID>
14:56:33.418 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 1 (size=1009, ref allele: G)
14:56:33.419 WARN  FuncotatorUtils - createAminoAcidSequence given a coding sequence of length not divisible by 3.  Dropping bases from the end: 1 (size=1009, alt allele: A)