learn_orientation: Learn Read Orientation Model (Mutect2)

In TearsWillFall/variantCall: An implementation of a wrapper for variant calling using MuTECT2 and Platypus GNU/Unix based systems

Description

This function takes a f1r2 read information and generates an orientation model to be used for further filtering steps.

Usage

learn_orientation(
  bin_path = "tools/gatk/gatk",
  f1r2 = "",
  f1r2_dir = "",
  output_name = "",
  output_dir = "",
  verbose = FALSE
)

Arguments

bin_path	REQUIRED Path to GATK binary. Default tools/htslib/tabix.
f1r2	OPTIONAL Path to f1r2 file. Only if f1r2_dir is not given.
f1r2_dir	OPTIONAL Path to f1r2 file dir. Only if f1r2 is not given.
verbose	Optional Enables progress messages. Default False.

TearsWillFall/variantCall documentation built on Oct. 15, 2021, 8:51 p.m.