Output Formats Guide

VarAnnote supports multiple output formats for different use cases.

Supported Formats

JSON Format

Default format with full annotation data:

annotator.export_json(results, "output.json")

CSV Format

Tabular format for spreadsheet applications:

annotator.export_csv(results, "output.csv")

TSV Format

Tab-separated values:

annotator.export_tsv(results, "output.tsv")

Excel Format

Microsoft Excel format with multiple sheets:

annotator.export_excel(results, "output.xlsx")

VCF Format

Annotated VCF with INFO fields:

annotator.export_vcf(results, "output.vcf")

XML Format

Structured XML output:

annotator.export_xml(results, "output.xml")

Parquet Format

High-performance columnar format:

annotator.export_parquet(results, "output.parquet")

Format Options

Include Metadata

annotator.export_json(results, "output.json", include_metadata=True)

Custom Fields

fields = ["chr", "pos", "ref", "alt", "clinvar.significance"]
annotator.export_csv(results, "output.csv", fields=fields)

Compression

annotator.export_json(results, "output.json.gz", compress=True)