bamsurgeon
bamsurgeon [options]
Print a brief help message and exit.
Print the version number.
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:
Generate a skeleton YAML config file with all fields for the user to fill in.
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.
Typical usage:
bamsurgeon --config /path/to/config.yaml
Christopher Lalansingh - Boutros Lab
Shadrielle Melijah G. Espiritu - Boutros Lab
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
To install NGS::Tools::BAMSurgeon, copy and paste the appropriate command in to your terminal.
cpanm
cpanm NGS::Tools::BAMSurgeon
CPAN shell
perl -MCPAN -e shell install NGS::Tools::BAMSurgeon
For more information on module installation, please visit the detailed CPAN module installation guide.