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GATK4 Funcotator generated annotation differs from dbSNP
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-126.96.36.199/gatk-package-188.8.131.52-local.jar 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:
When I checked dbSNP for this variant (https://www.ncbi.nlm.nih.gov/snp/rs2288481), it suggests
a codon change GAA > AAA and corresponding amino acid change E>K.
Please note: I also ran GATK184.108.40.206 for Funcotator, but results are same as GATK220.127.116.11