NAME

bamsurgeon

SYNOPSIS

bamsurgeon [options]

OPTIONS

--help

Print a brief help message and exit.

--version

Print the version number.

--config

Configuration file in YAML format that contains the signatures information. Sample format:

--- signature_file: ../t/signatures.txt cancer_file: ../t/cancer_signatures.yaml vcf_file: signatures: Signature 5: 0.75 Signature 1A: 0.25 cancer:

--make_yaml

Generate a skeleton YAML config file with all fields for the user to fill in.

DESCRIPTION

This script initiates NGS::Tools::BAMSurgeon, which is a pipeline wrapper for BAMSurgeon (https://github.com/adamewing/bamsurgeon) and provides additional functionality for the simulation of copy number abberations in the tumour.

EXAMPLE

Typical usage:

bamsurgeon --config /path/to/config.yaml

AUTHORS

Christopher Lalansingh - Boutros Lab

Shadrielle Melijah G. Espiritu - Boutros Lab

ACKNOWLEDGEMENTS

Paul Boutros, Phd, PI - Boutros Lab

Lydia Liu - Boutros Lab

Takafumi Yamaguchi - Boutros Lab

Srinivasan Sivanandan - Boutros Lab

Adam D. Ewing - BAMSurgeon author

The Ontario Institute for Cancer Research