SnpEff: SnpEff

In mdelcorvo/rgumbo: A soup of useful R functions for genomics data analysis

SnpEff

Description

Function to make the SnpEff-based vcf readable by extracting the functional annotation and splitting each gene transcript into single rows.

Usage

SnpEff(vcf,modifier=F,amino=F,rm_dup=T)

Arguments

vcf	SnpEff-based annotated vcf file
modifier	if TRUE variants with no impact on gene will be removed
amino	if TRUE variants that do not change the amino acid sequence will be removed
rm_dup	if TRUE duplicated transcripts for each variant will be removed

Examples

SnpEff(vcf,modifier=F,amino=F,rm_dup=T)

mdelcorvo/rgumbo documentation built on Jan. 3, 2025, 2:12 p.m.