---
name: "genome-music-play"
section: "1p"
platform: "linux"
package: "libgenome-model-tools-music-perl"
version: "0.04-4"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/genome-music-play"
---

# genome-music-play(1p)

Run the full suite of MuSiC tools sequentially.

## genome music play

## NAME

genome music play - Run the full suite of MuSiC tools sequentially.

## VERSION

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

## SYNOPSIS

genome music play --bam-list=? --roi-file=? --reference-sequence=? --output-dir=? --maf-file=? --pathway-file=? \[--numeric-clinical-data-file=?\] \[--categorical-clinical-data-file=?\] \[--mutation-matrix-file=?\] \[--permutations=?\] \[--normal-min-depth=?\] \[--tumor-min-depth=?\] \[--min-mapq=?\] \[--show-skipped\] \[--genes-to-ignore=?\] \[--bmr=?\] \[--max-proximity=?\] \[--bmr-modifier-file=?\] \[--numerical-data-test-method=?\] \[--skip-low-mr-genes\] \[--max-fdr=?\] \[--genetic-data-type=?\] \[--wu-annotation-headers\] \[--bmr-groups=?\] \[--separate-truncations\] \[--merge-concurrent-muts\] \[--skip-non-coding\] \[--skip-silent\] \[--min-mut-genes-per-path=?\] \[--glm-model-file=?\] \[--processors=?\] \[--aa-range=?\] \[--nuc-range=?\] \[--reference-build=?\] \[--show-known-hits\] \[--glm-clinical-data-file=?\] \[--use-maf-in-glm\] \[--omimaa-dir=?\] \[--cosmic-dir=?\] \[--verbose\] \[--clinical-correlation-matrix-file=?\]

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 \[sample\_name normal\_bam tumor\_bam\]

- roi-file *Text*

  Tab delimited list of ROIs \[chr start stop gene\_name\]

- reference-sequence *Text*

  Path to reference sequence in FASTA format

- output-dir *Text*

  Directory where output files and subdirectories will be written

- maf-file *Text*

  List of mutations using TCGA MAF specifications v2.3

- pathway-file *Text*

  Tab-delimited file of pathway information

## OPTIONAL ARGUMENTS

- 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)