filter_snv: Filter somatic single nucleotide variants.

In rdeborja/ShlienLab.Core.SSM: Simple Somatic Mutation (SSM) library.

Description

Apply the standard set of single nucleotide variant filters on a dataframe generated by the ShlienLab SSM pipeline.

Usage

filter_snv(data = NULL, coverage = TRUE, source = "WXS", exac = 0.001, vaf = 0)

Arguments

data	R dataframe from the ShlienLab SSM pipeline (required).
coverage	Filter based on coverage criteria from library type defined in source (default: TRUE).
source	Type of library sequenced (default: WXS – Must be one of WGS, WXS, CPANEL)
exac	ExAC threshold (default: 0.01)
vaf	VAF threshold (default: 0.0)

Value

Returns a dataframe containing only SNV mutations that have been filtered using the standard set of lab filters.

Author(s)

Richard J. de Borja

rdeborja/ShlienLab.Core.SSM documentation built on May 20, 2019, 5:27 p.m.