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GMT-MUSIC-GALAXY(1p) User Contributed Perl Documentation GMT-MUSIC-GALAXY(1p)

gmt music galaxy

NAME

gmt music galaxy - Run the full suite of MuSiC tools sequentially.

VERSION

This document describes gmt music galaxy version 0.04 (2018-07-05 at 09:17:13)

SYNOPSIS

gmt 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

Tab delimited list of BAM files [sample_name normal_bam tumor_bam]
Location where Galaxy would like the bundle of Music outputs to be saved
Tab delimited list of ROIs [chr start stop gene_name]
Path to reference sequence in FASTA format
List of mutations using TCGA MAF specifications v2.3
Tab-delimited file of pathway information

OPTIONAL ARGUMENTS

Directory where output files and subdirectories will be written

Default value '' if not specified

Table of samples (y) vs. numeric clinical data category (x)
Table of samples (y) vs. categorical clinical data category (x)
Optionally store the sample-vs-gene matrix used during calculations.
Number of permutations used to determine P-values
The minimum read depth to consider a Normal BAM base as covered
The minimum read depth to consider a Tumor BAM base as covered
The minimum mapping quality of reads to consider towards read depth counts
Report each skipped mutation, not just how many

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

Make show-skipped 'false'
Comma-delimited list of genes to ignore for background mutation rates
Background mutation rate in the targeted regions
Maximum AA distance between 2 mutations
Tab delimited list of values per gene that modify BMR before testing [gene_name bmr_modifier]
Either 'cor' for Pearson Correlation or 'wilcox' for the Wilcoxon Rank-Sum Test for numerical clinical data.

Default value 'cor' if not specified

Skip testing genes with MRs lower than the background MR

Default value 'true' if not specified

Make skip-low-mr-genes 'false'
The maximum allowed false discovery rate for a gene to be considered an SMG

Default value '0.2' if not specified

Data in matrix file must be either "gene" or "variant" type data
Use this to default to wustl annotation format headers
Make wu-annotation-headers 'false'
Number of clusters of samples with comparable BMRs

Default value '1' if not specified

Group truncational mutations as a separate category

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

Make separate-truncations 'false'
Multiple mutations of a gene in the same sample are treated as 1

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

Make merge-concurrent-muts 'false'
Skip non-coding mutations from the provided MAF file

Default value 'true' if not specified

Make skip-non-coding 'false'
Skip silent mutations from the provided MAF file

Default value 'true' if not specified

Make skip-silent 'false'
Pathways with fewer mutated genes than this will be ignored

Default value '1' if not specified

File outlining the type of model, response variable, covariants, etc. for the GLM analysis. (See DESCRIPTION).
Number of processors to use in SMG (requires 'foreach' and 'doMC' R packages)

Default value '1' if not specified

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

Default value '2' if not specified

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

Default value '5' if not specified

Put either "Build36" or "Build37"

Default value 'Build37' if not specified

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

Default value 'true' if not specified

Make show-known-hits 'false'
Clinical traits, mutational profiles, other mixed clinical data (See DESCRIPTION).
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

Make use-maf-in-glm 'false'
omim amino acid mutation database folder
cosmic amino acid mutation database folder
turn on to display larger working output

Default value 'true' if not specified

Make verbose 'false'
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)

2018-07-05 perl v5.26.2