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