run_snv_filter_postprocessing: Run the SNV filter postprocessing function.

In shlienlab/ShlienLab.Core.Filter: ShlienLab.Core.Filter

Description

A function that wraps the SNV filter postprocessing pipeline.

Usage

run_snv_filter_postprocessing(data = NULL, cfilter = NULL, min.dist.complex = 0, max_number_of_flagged = 2, pon = NULL, pon_max = 2, hardfilter = FALSE)

Arguments

data	somatic mutation dataframe (required)
cfilter	output file from the cfilter pipeline (required)
min.dist.complex	minimum distance to complex region to be considered overlap (optional, default: 0)
max_number_of_flagged	maximum number of "FLAGGED" tag in all filters (optional, default=2)
pon	full path to the panel of normal count table (required)
pon_max	minimum number of recurrence within panel of normals (optional, default=2)
hardfilter	flag to issue when removing filtered mutations instead of annotating

Value

Returns a dataframe with hard-filtered mutations and annotations.

Author(s)

Richard J. de Borja <[e-mail]>

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