Extracts snpeff annotations from vcf

Will take a vcf with snpeff annotations and output a list of two dataframes.

Usage

format_snpeff_annotations(vcfpath)

Arguments

vcfpath

path to vcf file

Value

A list of two dataframes:

• final_snp_impacts: one row per snp, has the highest impact of any transcript for that snp indicated

• formatted_snpeff_annotations: one row per transcript. snps will have multiple transcripts identified by snpeff.

The IMPACT_PLUS column has had modifier snps broken out into intergenic and coding modifiers.

Examples

# work in progress