genome music galaxy

VERSION

This document describes genome music galaxy version 0.04 (2013-05-14 at 16:03:04)

SYNOPSIS

genome music galaxy [--output-dir=?] --bam-list=? --output-bundle=? --roi-file=? --reference-sequence=? --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 \s-1BAM\s0 files [sample_name normal_bam tumor_bam]

output-bundle Text

Location where Galaxy would like the bundle of Music outputs to be saved

roi-file Text

Tab delimited list of ROIs [chr start stop gene_name]

reference-sequence Text

Path to reference sequence in \s-1FASTA\s0 format

maf-file Text

List of mutations using \s-1TCGA\s0 \s-1MAF\s0 specifications v2.3

pathway-file Text

Tab-delimited file of pathway information

OPTIONAL ARGUMENTS

output-dir

Directory where output files and subdirectories will be written Default value '' if not specified

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 \s-1BAM\s0 base as covered

tumor-min-depth Integer

The minimum read depth to consider a Tumor \s-1BAM\s0 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

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 \s-1AA\s0 distance between 2 mutations

bmr-modifier-file Text

Tab delimited list of values per gene that modify \s-1BMR\s0 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 \s-1MR\s0 Default value 'true' if not specified

max-fdr Number

The maximum allowed false discovery rate for a gene to be considered an \s-1SMG\s0 Default value '0.2' if not specified

genetic-data-type Text

Data in matrix file must be either \*(L"gene\*(R" or \*(L"variant\*(R" type data

wu-annotation-headers Boolean

Use this to default to wustl annotation format headers

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

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

skip-non-coding Boolean

Skip non-coding mutations from the provided \s-1MAF\s0 file Default value 'true' if not specified

skip-silent Boolean

Skip silent mutations from the provided \s-1MAF\s0 file Default value 'true' if not specified

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 \s-1GLM\s0 analysis. (See \s-1DESCRIPTION\s0).

processors Integer

Number of processors to use in \s-1SMG\s0 (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 \*(L"Build36\*(R" or \*(L"Build37\*(R" Default value 'Build37' if not specified

show-known-hits Boolean

When a finding is novel, show known \s-1AA\s0 in that gene Default value 'true' if not specified

glm-clinical-data-file Text

Clinical traits, mutational profiles, other mixed clinical data (See \s-1DESCRIPTION\s0).

use-maf-in-glm Boolean

Set this flag to use the variant matrix created from the \s-1MAF\s0 file as variant input to \s-1GLM\s0 analysis. Default value 'false' (--nouse-maf-in-glm) if not specified

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

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).

RELATED TO genome-music-galaxy…

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)