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Official code repository for GATK versions 4 and up
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GATK4 Funcotator generated annotation differs from dbSNP #6009

Open bhanugandham opened 5 years ago

bhanugandham commented 5 years ago

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-4.1.0.0/gatk-package-4.1.0.0-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:

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 (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 GATK4.1.2.0 for Funcotator, but results are same as GATK4.1.0.0

This Issue was generated from your forums

bhanugandham commented 5 years ago

Hi @jonn-smith I created a bug report for this as suggested during GATK office hrs.