variant_annotation.md

VARIANT ANNOTATION - GATK4 Funcotator

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Table of contents

• VARIANT ANNOTATION - GATK4 Funcotator
  • Table of contents
  • Variant annotation process
    • 1. Functional annotation workflow
    • 2. Germline pre-packaged data sources
    • 3. GATK4 Funcotator
    • 4. Extract fields from VCF file to a tab-delimited table

Variant annotation process

1. Functional annotation workflow

flowchart TD
    subgraph "VARIANT ANNOTATION"
    A("Analysis-Ready Variants<br>SNVs + Indels")--> B[[Funcotator]] --> C{{"Functionally<br>Annotated Variants"}} --> D(["Further analysis"])
    style A fill:#34495e,stroke:#333,stroke-width:4px,color:#fff
    style B fill:#228B22,stroke:#333,stroke-width:4px,color:#ADD8E6
    style C fill:#767076,stroke:#F9F2F4,stroke-width:2px,color:#fff
    end

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2. Germline pre-packaged data sources

./gatk FuncotatorDataSourceDownloader --germline --validate-integrity --extract-after-download

3. GATK4 Funcotator

# Set up relevant absolute path
variant="path/to/variant_calling"
reference="path/to/reference/UCSC_hg38/chr21.fa.gz"
dataSources="path/to/reference/funcotator_dataSources.v1.7.20200521g/"
annotation="path/to/annotation"
results="path/to/results"

gatk --java-options "-Xmx4G" Funcotator \
    -V "${variant}/chr21_tumor_cnn_filtered.vcf" \
    -R "${reference}" \
    -O "${annotation}/chr21_tumor_funcotated.vcf" \
    --output-file-format VCF \
    --data-sources-path ${dataSources} \
    --ref-version hg38

4. Extract fields from VCF file to a tab-delimited table

gatk VariantsToTable \
    -V "${annotation}/chr21_tumor_funcotated.vcf" -F AC -F AN -F DP -F AF -F FUNCOTATION \
    -O "${results}/chr21_tumor_output.table"