GATK4 Funcotator generated annotation differs from dbSNP
open | Created 2019-06-17 | Last updated 2019-06-17| Posted by bhanugandham | See in Github

Funcotator Vanilla bug

User report:
I wanted to get functional annotation of variants identified in earlier steps of my analysis. I thought of using Funcotator for this purpose. Interestingly, the annotation differed from that on dbSNP. Can anyone help me to understand why is there a difference?
Below is the command that I executed:
/usr/bin/java -jar gatk- Funcotator --variant chr19_49374939.vcf --data-sources-path GRCh38/FuncotatorDataSources/funcotator_dataSources.v1.6.20190124g --ref-version hg38 --reference GRCh38/genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa --tmp-dir tmp --output chr19_49374939.FuncotatorAnnotated_GATK4100.vcf --output-file-format VCF

The input VCF file contains a variant: chr19 49374939 rs2288481 G>A

Funcotator provides the following annotation:

DKKL1|hg38|chr19|49374939|49374939|MISSENSE||SNP|G|G|A|g.chr19:49374939G>A|ENST00000221498.6|+|5|1045|c.640G>A|c.(640-642)Ggg>Agg|p.G214R| ...

When I checked dbSNP for this variant (, it suggests

a codon change GAA > AAA and corresponding amino acid change E>K.

Please note: I also ran GATK4.1.2.0 for Funcotator, but results are same as GATK4.1.0.0

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