call_segments: Call segments for panel, exome and WGS data using CNVkit This...

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

Description

Call segments for panel, exome and WGS data using CNVkit This function takes a single or multiple tumor samples and a single or multiple normal samples, creates a reference of a pool of normal samples, estimates the coverage and normalizes its log2 ratio using gc and accessibility information. Ultimately, it calls the segments of binned data and identifies the state of CNA.

Usage

call_segments(
  bin_path = "~/tools/cnvkit/cnvkit.py",
  tumor_samples = "",
  normal_samples = "",
  pool_ref = "",
  targets = "",
  fasta = "",
  access = "",
  ref_output = "",
  output_dir = "",
  diagram = TRUE,
  scatter = TRUE,
  threads = 3,
  verbose = FALSE,
  male = TRUE
)

Arguments

bin_path	Path to cnvkit binary.
tumor_samples	REQUIRED Path to tumor samples bam files. For multiple samples pass as vector with their paths.
normal_samples	OPTIONAL Path to normal samples bam files. For multiple samples pass as vector with their paths. Used to create a reference.
pool_ref	OPTIONAL Path to reference of normals. Needs to be generated beforehand from normals/normals
targets	OPTIONAL Path to exome capture targets. Required if targeted or panel.
access	OPTIONAL Path to bed with accessibility information.
ref_output	OPTIONAL Name of the reference file output.
output_dir	OPTIONAL Path to the output directory.
diagram	DEFAULT==TRUE Plot diagram of segments.
scatter	DEFAULT==TRUE Plot scatter plot of segments.
threads	DEFAULT==3 Number of threads to use.
verbose	DEFAULT==FALSE Enables progress messages.
male	DEFAULT==TRUE Reference is a male.

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