NAME

generate_signature.pl

SYNOPSIS

generate_signature.pl [options] [file ...]

        Options:
        --help                          brief help message
        --man                           full documentation
        --config                        configuration file in YAML format containing signature information (Required)
        --chromosome        the chromosome that mutations are generated for (Required)
        --cb_bed            the bed file for the callable bases of the chromosome (default = "None")
        --mut_num                       number of sites to generate (default = 0)
        --mut_rate                      rate of mutation to generate (default = 0)
        --seed              seed used for reproducible random mutation location generation (default = "None")
        --mut_file          file to output mutations to (default = "./mut_file.txt")
        --minvaf            minimum variant allele fraction (default = 0.25)
        --maxvaf            maximum variant allele fraction (default = 0.5)
        --vafbeta1          left shape parameter for beta distribution of VAFs (default = 2.0)
        --vafbeta2          right shape parameter for beta distribution of VAFs (default = 2.0)

OPTIONS

--help

Print a brief help message and exit.

--man

Print the manual page.

--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:

--chromosome

The chromosome that mutations are generated for.

--cb_bed

The bed file for the callable bases of the chromosome.

--mut_num

Number of sites to generate. Overwrite mut_rate and cancer mutation rate.

--mut_rate

Rate of mutation to generate. Overwrite cancer mutation rate.

--seed

Seed used for reproducible random mutation location generation.

--mut_file

File to output mutations to.

--minvaf

Minimum variant allele fraction.

--maxvaf

Maximum variant allele fraction.

--vafbeta1

Left shape parameter for beta distribution of VAFs.

--vafbeta2

Right shape parameter for beta distribution of VAFs.

DESCRIPTION

generate_signature.pl Generate mutation file with specified signatures.

 Generate mutation input varfile according to the Trinucleotide Signature and Proportions specified
 - read the signatures file table for mutation types and probabilities
 - calculate mutation number and probabilities for each signature specified
 - randomly choose positions in the chromosome according to mutation type
 - specify chromosome, start, end, vaf, and alternative base in BEDfile format as output (varfile)
 - take in custome mutations vcf file and incorporate according to chromosome
 - take in cancer file and cancer name to generate cancer proportioned mutations and rates
 - take in covered bases bed file and only spike in mutation in bases with over 10x coverage

EXAMPLE

Typical usage:

AUTHOR

Lydia Liu

Boutros Lab The Ontario Institute for Cancer Research

ACKNOWLEDGEMENTS

Paul Boutros, PhD, PI -- Boutros Lab

Takafumi Yamaguchi -- Boutros Lab

Srinivasan Sivanandan -- Boutros Lab

Adam D. Ewing -- BAMSurgeon author

SEE ALSO

BAMsurgeon.pl