NAME

NGS::Tools::BAMSurgeon

VERSION

Version 1.0.0

DESCRIPTION

This package 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.

DEPENDENCIES

• samtools (>= 1.1)

• picardtools (>= 1.130)

• python (2.7.x)

• bamsurgeon (1.0)

• bwa (>= 0.7.12)

• novocraft (>= 3.02.12)

• velvet (>= 1.0.13)

• exonerate (>= 2.2.0)

• alleleCount (>= 2.1.1)

• bedtools (>= 2.24.0)

USAGE

use NGS::Tools::BAMSurgeon;

my $bamsurgeon = NGS::Tools::BAMSurgeon->new(
	working_dir => '/path/to/working/dir',
	config => "path/to/config.yaml",
	somatic_profile => "path/to/somatic.yaml",
	germline_profile => "path/to/germ_mut.yaml",
	bam => 'test.bam',
	tumour_name => "test",
	sex => 'M',
	gpercent => 0.7,
	seed => 12345,
	# parameters for choosing mutations to spike in
	minvaf => 1,
	maxvaf => 1,
	vafbeta1 => 2.0,
	vafbeta2 => 2.0,
	indel_minlen => 1,
	indel_maxlen => 90,
	indel_types => 'INS,DEL',
	sv_minlen => 3000,
	sv_maxlen => 30000,
	sv_types => 'DUP,INV',
	phasing => 0,
	redochrs => 'all'
	);

$bamsurgeon->run(
	splitbam => 0,
	preparef => 0,
	pickgermmut => 0,
	germsim => 0,
	generatecallable => 0,
	picksomaticmut => 1,
	picktrinucleotides => 1,
	splitsubclones => 1,
	somaticsim => 1,
	makevcf => 1,
	extractleafs => 1,
	mergephases => 1,
	mergechromosomes => 1,
	mergefinal => 1,
	allelecount => 1
	);

METHODS

new

This subroutine creates a NGS::Tools::BAMSurgeon object with the following parameters (mandatory parameters are denoted with 1, optional with 0, or having a default specified, as per Params::Validate specifications):

config => 1,
somatic_profile => 1,
germline_profile => 1,
bam => 1,
sex => 1,
gpercent => 1,
seed => 0,
minvaf => 1,
maxvaf => 1,
vafbeta1 => { default => 2.0 },
vafbeta2 => { default => 2.0 },
indel_minlen => { default =>  1 },
indel_maxlen => { default => 90 },
indel_types => { default => 'INS,DEL' },
sv_minlen => { default => 3000 },
sv_maxlen => { default => 30000 },
sv_types => { default => 'DUP,INV,DEL' },
working_dir => { default => '.' },
tumour_name => { default => 'sm' },
log_dir => 0,
modules => 0,
phasing => 1,
redochrs => { default => 'all' }

run

This subroutine executes the pipeline with the parameters specified when the NGS::Tools::BAMSurgeon object is created. Stages can be turned on/off using the following parameters:

splitbam => 0,
preparef => 0,
pickgermmut => 0,
germsim => 0,
generatecallable => 0,
picksomaticmut => 0,
picktrinucleotides => 0,
somaticsim => 0,
makevcf => 0,
extractleafs => 0,
mergephases => 0,
mergechromosomes => 0,
mergefinal => 0,
allelecount => 0

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