run_snv_filter_postprocessing: Run the SNV filter postprocessing function.

Description Usage Arguments Value Author(s)

Description

A function that wraps the SNV filter postprocessing pipeline.

Usage

1
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 <richard.deborja@sickkids.ca>


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