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.

References

"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.

Examples

# work in progress