parse_pangolin: Parse VCF output file from pangolin as table

In TRON-Bioinformatics/splice2neo: Aberrant splice junction analysis with associated mutations

Parse VCF output file from pangolin as table

Description

requires the vcfR package.

Usage

parse_pangolin(vcf_file)

Arguments

vcf_file

path to a single VCF file, the output of pangolin

Value

a tibble with one row per variant annotation. Each input variant can have multiple annotations.

Examples

pangolin_file <- system.file("extdata", "spliceai_output.pangolin.vcf", package = "splice2neo")
parse_pangolin(pangolin_file)

TRON-Bioinformatics/splice2neo documentation built on March 25, 2024, 2:27 a.m.