Provided by: libgenome-model-tools-music-perl_0.04-4_all bug

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 (2018-07-05 at 09:17:13)

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

       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)