Run the full suite of music tools sequentially.
This document describes genome music play version 0.04 (2013-05-14 at 16:03:04)
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
Tab delimited list of \s-1BAM\s0 files [sample_name normal_bam tumor_bam]
Tab delimited list of ROIs [chr start stop gene_name]
Path to reference sequence in \s-1FASTA\s0 format
Directory where output files and subdirectories will be written
List of mutations using \s-1TCGA\s0 \s-1MAF\s0 specifications v2.3
Tab-delimited file of pathway information
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 \s-1BAM\s0 base as covered
The minimum read depth to consider a Tumor \s-1BAM\s0 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
Comma-delimited list of genes to ignore for background mutation rates
Background mutation rate in the targeted regions
Maximum \s-1AA\s0 distance between 2 mutations
Tab delimited list of values per gene that modify \s-1BMR\s0 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 \s-1MR\s0 Default value 'true' if not specified
The maximum allowed false discovery rate for a gene to be considered an \s-1SMG\s0 Default value '0.2' if not specified
Data in matrix file must be either \*(L"gene\*(R" or \*(L"variant\*(R" type data
Use this to default to wustl annotation format headers
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
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 mutations from the provided \s-1MAF\s0 file Default value 'true' if not specified
Skip silent mutations from the provided \s-1MAF\s0 file Default value 'true' if not specified
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 \s-1GLM\s0 analysis. (See \s-1DESCRIPTION\s0).
Number of processors to use in \s-1SMG\s0 (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 \*(L"Build36\*(R" or \*(L"Build37\*(R" Default value 'Build37' if not specified
When a finding is novel, show known \s-1AA\s0 in that gene Default value 'true' if not specified
Clinical traits, mutational profiles, other mixed clinical data (See \s-1DESCRIPTION\s0).
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
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
Optionally store the sample-vs-gene matrix used internally during calculations.
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.
Thomas B. Mooney, M.S.
Please see the credits for genome-music(1).
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)