garnish_variants: Process VCF variants and return a data table for epitope...

In andrewrech/antigen.garnish: Tumor neoantigen prediction

Process VCF variants and return a data table for epitope prediction.

Description

Process paired tumor-normal VCF variants annotated with SnpEff for neoantigen prediction using garnish_affinity. All versioned Ensembl transcript IDs (e.g. ENST00000311936.8) from any GRCh38 or GRCm38 release are supported. Parsing will fall back to using RefSeq IDs, but RefSeq IDs are not preferred.

Usage

garnish_variants(vcfs, tumor_sample_name = "TUMOR")

Arguments

vcfs	Paths to one or more VFC files to import. See details below.
tumor_sample_name	Character, name of column in vcf of tumor sample.

Value

A data table with one unique SnpEff variant annotation per row, including:

• sample_id: sample identifier constructed from input .vcf file names

• ANN: SnpEff annotation

• effect_type: SnpEff effect type

• transcript_id: transcript effected

• cDNA_change: cDNA change in HGVS format

See Also

garnish_affinity

garnish_antigens

andrewrech/antigen.garnish documentation built on July 8, 2022, 5:19 p.m.