Provided by: libgenome-model-tools-music-perl_0.04-1_all
genome music galaxy
NAME
genome music galaxy - Run the full suite of MuSiC tools sequentially.
VERSION
This document describes genome music galaxy version 0.04 (2013-05-25 at 17:45:01)
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 BAM 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 FASTA format maf-file Text List of mutations using TCGA MAF 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 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 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 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 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 MAF file Default value 'true' if not specified skip-silent Boolean Skip silent mutations from the provided MAF 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 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 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 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).
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)