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.\" ========================================================================
.\"
.IX Title "GENOME-MUSIC-PLAY 1p"
.TH GENOME-MUSIC-PLAY 1p "2018-07-05" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "genome music play"
.IX Header "genome music play"
.SH "NAME"
genome music play \- Run the full suite of MuSiC tools sequentially.
.SH "VERSION"
.IX Header "VERSION"
This document describes genome music play version 0.04 (2018\-07\-05 at 09:17:13)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
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=?]
.PP
This tool takes as parameters all the information required to run the individual tools. An example usage is:
.PP
.Vb 9
\& ... music play \e
\&        \-\-bam\-list input/bams_to_analyze.txt \e
\&        \-\-numeric\-clinical\-data\-file input/numeric_clinical_data.csv \e
\&        \-\-maf\-file input/myMAF.tsv \e
\&        \-\-output\-dir play_output_dir \e
\&        \-\-pathway\-file input/pathway_db \e
\&        \-\-reference\-sequence input/refseq/all_sequences.fa \e
\&        \-\-roi\-file input/all_coding_regions.bed \e
\&        \-\-genetic\-data\-type gene
.Ve
.SH "REQUIRED ARGUMENTS"
.IX Header "REQUIRED ARGUMENTS"
.IP "bam-list  \fIText\fR" 4
.IX Item "bam-list Text"
Tab delimited list of \s-1BAM\s0 files [sample_name normal_bam tumor_bam]
.IP "roi-file  \fIText\fR" 4
.IX Item "roi-file Text"
Tab delimited list of ROIs [chr start stop gene_name]
.IP "reference-sequence  \fIText\fR" 4
.IX Item "reference-sequence Text"
Path to reference sequence in \s-1FASTA\s0 format
.IP "output-dir  \fIText\fR" 4
.IX Item "output-dir Text"
Directory where output files and subdirectories will be written
.IP "maf-file  \fIText\fR" 4
.IX Item "maf-file Text"
List of mutations using \s-1TCGA MAF\s0 specifications v2.3
.IP "pathway-file  \fIText\fR" 4
.IX Item "pathway-file Text"
Tab-delimited file of pathway information
.SH "OPTIONAL ARGUMENTS"
.IX Header "OPTIONAL ARGUMENTS"
.IP "numeric-clinical-data-file  \fIText\fR" 4
.IX Item "numeric-clinical-data-file Text"
Table of samples (y) vs. numeric clinical data category (x)
.IP "categorical-clinical-data-file  \fIText\fR" 4
.IX Item "categorical-clinical-data-file Text"
Table of samples (y) vs. categorical clinical data category (x)
.IP "mutation-matrix-file  \fIText\fR" 4
.IX Item "mutation-matrix-file Text"
Optionally store the sample-vs-gene matrix used during calculations.
.IP "permutations  \fINumber\fR" 4
.IX Item "permutations Number"
Number of permutations used to determine P\-values
.IP "normal-min-depth  \fIInteger\fR" 4
.IX Item "normal-min-depth Integer"
The minimum read depth to consider a Normal \s-1BAM\s0 base as covered
.IP "tumor-min-depth  \fIInteger\fR" 4
.IX Item "tumor-min-depth Integer"
The minimum read depth to consider a Tumor \s-1BAM\s0 base as covered
.IP "min-mapq  \fIInteger\fR" 4
.IX Item "min-mapq Integer"
The minimum mapping quality of reads to consider towards read depth counts
.IP "show-skipped  \fIBoolean\fR" 4
.IX Item "show-skipped Boolean"
Report each skipped mutation, not just how many
.Sp
Default value 'false' (\-\-noshow\-skipped) if not specified
.IP "noshow-skipped  \fIBoolean\fR" 4
.IX Item "noshow-skipped Boolean"
Make show-skipped 'false'
.IP "genes-to-ignore  \fIText\fR" 4
.IX Item "genes-to-ignore Text"
Comma-delimited list of genes to ignore for background mutation rates
.IP "bmr  \fINumber\fR" 4
.IX Item "bmr Number"
Background mutation rate in the targeted regions
.IP "max-proximity  \fIText\fR" 4
.IX Item "max-proximity Text"
Maximum \s-1AA\s0 distance between 2 mutations
.IP "bmr-modifier-file  \fIText\fR" 4
.IX Item "bmr-modifier-file Text"
Tab delimited list of values per gene that modify \s-1BMR\s0 before testing [gene_name bmr_modifier]
.IP "numerical-data-test-method  \fIText\fR" 4
.IX Item "numerical-data-test-method Text"
Either 'cor' for Pearson Correlation or 'wilcox' for the Wilcoxon Rank-Sum Test for numerical clinical data.
.Sp
Default value 'cor' if not specified
.IP "skip-low-mr-genes  \fIBoolean\fR" 4
.IX Item "skip-low-mr-genes Boolean"
Skip testing genes with MRs lower than the background \s-1MR\s0
.Sp
Default value 'true' if not specified
.IP "noskip-low-mr-genes  \fIBoolean\fR" 4
.IX Item "noskip-low-mr-genes Boolean"
Make skip-low-mr-genes 'false'
.IP "max-fdr  \fINumber\fR" 4
.IX Item "max-fdr Number"
The maximum allowed false discovery rate for a gene to be considered an \s-1SMG\s0
.Sp
Default value '0.2' if not specified
.IP "genetic-data-type  \fIText\fR" 4
.IX Item "genetic-data-type Text"
Data in matrix file must be either \*(L"gene\*(R" or \*(L"variant\*(R" type data
.IP "wu-annotation-headers  \fIBoolean\fR" 4
.IX Item "wu-annotation-headers Boolean"
Use this to default to wustl annotation format headers
.IP "nowu-annotation-headers  \fIBoolean\fR" 4
.IX Item "nowu-annotation-headers Boolean"
Make wu-annotation-headers 'false'
.IP "bmr-groups  \fIInteger\fR" 4
.IX Item "bmr-groups Integer"
Number of clusters of samples with comparable BMRs
.Sp
Default value '1' if not specified
.IP "separate-truncations  \fIBoolean\fR" 4
.IX Item "separate-truncations Boolean"
Group truncational mutations as a separate category
.Sp
Default value 'false' (\-\-noseparate\-truncations) if not specified
.IP "noseparate-truncations  \fIBoolean\fR" 4
.IX Item "noseparate-truncations Boolean"
Make separate-truncations 'false'
.IP "merge-concurrent-muts  \fIBoolean\fR" 4
.IX Item "merge-concurrent-muts Boolean"
Multiple mutations of a gene in the same sample are treated as 1
.Sp
Default value 'false' (\-\-nomerge\-concurrent\-muts) if not specified
.IP "nomerge-concurrent-muts  \fIBoolean\fR" 4
.IX Item "nomerge-concurrent-muts Boolean"
Make merge-concurrent-muts 'false'
.IP "skip-non-coding  \fIBoolean\fR" 4
.IX Item "skip-non-coding Boolean"
Skip non-coding mutations from the provided \s-1MAF\s0 file
.Sp
Default value 'true' if not specified
.IP "noskip-non-coding  \fIBoolean\fR" 4
.IX Item "noskip-non-coding Boolean"
Make skip-non-coding 'false'
.IP "skip-silent  \fIBoolean\fR" 4
.IX Item "skip-silent Boolean"
Skip silent mutations from the provided \s-1MAF\s0 file
.Sp
Default value 'true' if not specified
.IP "noskip-silent  \fIBoolean\fR" 4
.IX Item "noskip-silent Boolean"
Make skip-silent 'false'
.IP "min-mut-genes-per-path  \fIInteger\fR" 4
.IX Item "min-mut-genes-per-path Integer"
Pathways with fewer mutated genes than this will be ignored
.Sp
Default value '1' if not specified
.IP "glm-model-file  \fIText\fR" 4
.IX Item "glm-model-file Text"
File outlining the type of model, response variable, covariants, etc. for the \s-1GLM\s0 analysis. (See \s-1DESCRIPTION\s0).
.IP "processors  \fIInteger\fR" 4
.IX Item "processors Integer"
Number of processors to use in \s-1SMG\s0 (requires 'foreach' and 'doMC' R packages)
.Sp
Default value '1' if not specified
.IP "aa-range  \fIInteger\fR" 4
.IX Item "aa-range Integer"
Set how close a 'near' match is when searching for amino acid near hits
.Sp
Default value '2' if not specified
.IP "nuc-range  \fIInteger\fR" 4
.IX Item "nuc-range Integer"
Set how close a 'near' match is when searching for nucleotide position near hits
.Sp
Default value '5' if not specified
.IP "reference-build  \fIText\fR" 4
.IX Item "reference-build Text"
Put either \*(L"Build36\*(R" or \*(L"Build37\*(R"
.Sp
Default value 'Build37' if not specified
.IP "show-known-hits  \fIBoolean\fR" 4
.IX Item "show-known-hits Boolean"
When a finding is novel, show known \s-1AA\s0 in that gene
.Sp
Default value 'true' if not specified
.IP "noshow-known-hits  \fIBoolean\fR" 4
.IX Item "noshow-known-hits Boolean"
Make show-known-hits 'false'
.IP "glm-clinical-data-file  \fIText\fR" 4
.IX Item "glm-clinical-data-file Text"
Clinical traits, mutational profiles, other mixed clinical data (See \s-1DESCRIPTION\s0).
.IP "use-maf-in-glm  \fIBoolean\fR" 4
.IX Item "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.
.Sp
Default value 'false' (\-\-nouse\-maf\-in\-glm) if not specified
.IP "nouse-maf-in-glm  \fIBoolean\fR" 4
.IX Item "nouse-maf-in-glm Boolean"
Make use-maf-in-glm 'false'
.IP "omimaa-dir  \fIPath\fR" 4
.IX Item "omimaa-dir Path"
omim amino acid mutation database folder
.IP "cosmic-dir  \fIPath\fR" 4
.IX Item "cosmic-dir Path"
cosmic amino acid mutation database folder
.IP "verbose  \fIBoolean\fR" 4
.IX Item "verbose Boolean"
turn on to display larger working output
.Sp
Default value 'true' if not specified
.IP "noverbose  \fIBoolean\fR" 4
.IX Item "noverbose Boolean"
Make verbose 'false'
.IP "clinical-correlation-matrix-file  \fIText\fR" 4
.IX Item "clinical-correlation-matrix-file Text"
Optionally store the sample-vs-gene matrix used internally during calculations.
.SH "DESCRIPTION"
.IX Header "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.
.SH "AUTHORS"
.IX Header "AUTHORS"
.Vb 1
\& Thomas B. Mooney, M.S.
.Ve
.SH "CREDITS"
.IX Header "CREDITS"
Please see the credits for \fBgenome-music\fR(1).
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fBgenome-music\fR(1),
\&\fBgenome-music-path-scan\fR(1),
\&\fBgenome-music-smg\fR(1),
\&\fBgenome-music-clinical-correlation\fR(1),
\&\fBgenome-music-mutation-relation\fR(1),
\&\fBgenome-music-cosmic-omim\fR(1),
\&\fBgenome-music-proximity\fR(1),
\&\fBgenome-music-pfam\fR(1)