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genome :: music :: play

genome music play

NAME

genome music play - Run the full suite of MuSiC tools sequentially.


VERSION

This document describes genome music play version 0.0401 (2014-02-13 at 08:01:08)


SYNOPSIS

genome music play --bam-list=? --roi-file=? --reference-sequence=? --output-dir=? --maf-file=? --pathway-file=? [--numeric-clinical-data-file=?] [--categorical-clinical-data-file=?] [--mutation-matrix-file=?] [--permutations=?] [--normal-min-depth=?] [--tumor-min-depth=?] [--min-mapq=?] [--show-skipped] [--genes-to-ignore=?] [--bmr=?] [--max-proximity=?] [--bmr-modifier-file=?] [--numerical-data-test-method=?] [--skip-low-mr-genes] [--max-fdr=?] [--genetic-data-type=?] [--wu-annotation-headers] [--bmr-groups=?] [--separate-truncations] [--merge-concurrent-muts] [--skip-non-coding] [--skip-silent] [--min-mut-genes-per-path=?] [--glm-model-file=?] [--processors=?] [--aa-range=?] [--nuc-range=?] [--reference-build=?] [--show-known-hits] [--glm-clinical-data-file=?] [--use-maf-in-glm] [--omimaa-dir=?] [--cosmic-dir=?] [--verbose] [--clinical-correlation-matrix-file=?]

This tool takes as parameters all the information required to run the individual tools. An example usage is:

 ... music play \
        --bam-list input/bams_to_analyze.txt \
        --numeric-clinical-data-file input/numeric_clinical_data.csv \
        --maf-file input/myMAF.tsv \
        --output-dir play_output_dir \
        --pathway-file input/pathway_db \
        --reference-sequence input/refseq/all_sequences.fa \
        --roi-file input/all_coding_regions.bed \
        --genetic-data-type gene

REQUIRED ARGUMENTS

bam-list Text

Tab delimited list of BAM files [sample_name normal_bam tumor_bam]

roi-file Text

Tab delimited list of ROIs [chr start stop gene_name]

reference-sequence Text

Path to reference sequence in FASTA format

output-dir Text

Directory where output files and subdirectories will be written

maf-file Text

List of mutations using TCGA MAF specifications v2.3

pathway-file Text

Tab-delimited file of pathway information


OPTIONAL ARGUMENTS

numeric-clinical-data-file Text

Table of samples (y) vs. numeric clinical data category (x)

categorical-clinical-data-file Text

Table of samples (y) vs. categorical clinical data category (x)

mutation-matrix-file Text

Optionally store the sample-vs-gene matrix used during calculations.

permutations Number

Number of permutations used to determine P-values

normal-min-depth Integer

The minimum read depth to consider a Normal BAM base as covered

tumor-min-depth Integer

The minimum read depth to consider a Tumor BAM base as covered

min-mapq Integer

The minimum mapping quality of reads to consider towards read depth counts

show-skipped Boolean

Report each skipped mutation, not just how many

Default value 'false' (--noshow-skipped) if not specified

noshow-skipped Boolean

Make show-skipped 'false'

genes-to-ignore Text

Comma-delimited list of genes to ignore for background mutation rates

bmr Number

Background mutation rate in the targeted regions

max-proximity Text

Maximum AA distance between 2 mutations

bmr-modifier-file Text

Tab delimited list of values per gene that modify BMR before testing [gene_name bmr_modifier]

numerical-data-test-method Text

Either 'cor' for Pearson Correlation or 'wilcox' for the Wilcoxon Rank-Sum Test for numerical clinical data.

Default value 'cor' if not specified

skip-low-mr-genes Boolean

Skip testing genes with MRs lower than the background MR

Default value 'true' if not specified

noskip-low-mr-genes Boolean

Make skip-low-mr-genes 'false'

max-fdr Number

The maximum allowed false discovery rate for a gene to be considered an SMG

Default value '0.2' if not specified

genetic-data-type Text

Data in matrix file must be either "gene" or "variant" type data

wu-annotation-headers Boolean

Use this to default to wustl annotation format headers

nowu-annotation-headers Boolean

Make wu-annotation-headers 'false'

bmr-groups Integer

Number of clusters of samples with comparable BMRs

Default value '1' if not specified

separate-truncations Boolean

Group truncational mutations as a separate category

Default value 'false' (--noseparate-truncations) if not specified

noseparate-truncations Boolean

Make separate-truncations 'false'

merge-concurrent-muts Boolean

Multiple mutations of a gene in the same sample are treated as 1

Default value 'false' (--nomerge-concurrent-muts) if not specified

nomerge-concurrent-muts Boolean

Make merge-concurrent-muts 'false'

skip-non-coding Boolean

Skip non-coding mutations from the provided MAF file

Default value 'true' if not specified

noskip-non-coding Boolean

Make skip-non-coding 'false'

skip-silent Boolean

Skip silent mutations from the provided MAF file

Default value 'true' if not specified

noskip-silent Boolean

Make skip-silent 'false'

min-mut-genes-per-path Integer

Pathways with fewer mutated genes than this will be ignored

Default value '1' if not specified

glm-model-file Text

File outlining the type of model, response variable, covariants, etc. for the GLM analysis. (See DESCRIPTION).

processors Integer

Number of processors to use in SMG (requires 'foreach' and 'doMC' R packages)

Default value '1' if not specified

aa-range Integer

Set how close a 'near' match is when searching for amino acid near hits

Default value '2' if not specified

nuc-range Integer

Set how close a 'near' match is when searching for nucleotide position near hits

Default value '5' if not specified

reference-build Text

Put either "Build36" or "Build37"

Default value 'Build37' if not specified

show-known-hits Boolean

When a finding is novel, show known AA in that gene

Default value 'true' if not specified

noshow-known-hits Boolean

Make show-known-hits 'false'

glm-clinical-data-file Text

Clinical traits, mutational profiles, other mixed clinical data (See DESCRIPTION).

use-maf-in-glm Boolean

Set this flag to use the variant matrix created from the MAF file as variant input to GLM analysis.

Default value 'false' (--nouse-maf-in-glm) if not specified

nouse-maf-in-glm Boolean

Make use-maf-in-glm 'false'

omimaa-dir Path

omim amino acid mutation database folder

cosmic-dir Path

cosmic amino acid mutation database folder

verbose Boolean

turn on to display larger working output

Default value 'true' if not specified

noverbose Boolean

Make verbose 'false'

clinical-correlation-matrix-file Text

Optionally store the sample-vs-gene matrix used internally during calculations.


DESCRIPTION

This command can be used to run all of the MuSiC analysis tools on a set of data. Please see the individual tools for further description of the parameters.


AUTHORS

 Thomas B. Mooney, M.S.

CREDITS

Please see the credits for genome-music(1).


SEE ALSO

genome-music(1), genome-music-path-scan(1), genome-music-smg(1), genome-music-clinical-correlation(1), genome-music-mutation-relation(1), genome-music-cosmic-omim(1), genome-music-proximity(1), genome-music-pfam(1)



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