---
name: "Genome::Model::Tools::Music"
section: "3pm"
platform: "linux"
package: "libgenome-model-tools-music-perl"
version: "0.04-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Genome::Model::Tools::Music"
---

# Genome::Model::Tools::Music(3pm)

- 1\. mapped reads in BAM format

  - 2\. predicted or validated SNVs or indels in mutation annotation format (MAF)

  - 3\. a list of regions of interest (typically the boundaries of coding exons)

  - 4\. any relevant numeric or categorical clinical data.

  The formats for inputs 3. and 4. are:

- 3\. Regions of Interest File:

  - •

    Do not use headers

  - •

    4 columns, which are \[chromosome  start-position(1-based)  stop-position(1-based)  gene\_name\]

- 4\. Clinical Data Files:

  - •

    Headers are required

  - •

    At least 1 sample\_id column and 1 attribute column, with the format being \[sample\_id  clinical\_data\_attribute  clinical\_data\_attribute  ...\]

  - •

    The sample\_id must match the sample\_id listed in the MAF under "Tumor\_Sample\_Barcode" for relating the mutations of this sample.

  - •

    The header for each clinical\_data\_attribute will appear in the output file to denote relationships with the mutation data from the MAF.

Descriptions for the usage of each tool (each sub-command) can be found separately.

The **play** command runs all of the sub-commands serially on a selected input set.

EOS }

sub \_doc\_copyright\_years {\
     (2007,2011); }

sub \_doc\_license {\
     my `$self` = shift;\
     my (@y) = `$self`-\>\_doc\_copyright\_years;  \
     return \<\<EOS Copyright (C) `$y`\[0\]-$y\[1\] Washington University in St. Louis.

It is released under the Lesser GNU Public License (LGPL) version 3.  See the  associated LICENSE file in this distribution. EOS }

sub \_doc\_authors {\
     return \<\<EOS This software is developed by the analysis and engineering teams at  The Genome Institute at Washington University School of Medicine in St. Louis, with funding from the National Human Genome Research Institute.  Richard K. Wilson, P.I.

The primary authors of the MuSiC suite are:

```
 Nathan D. Dees, Ph.D.
 Cyriac Kandoth, Ph.D.
 Dan Koboldt, M.S.
 William Schierding, M.S.
 Michael Wendl, Ph.D.
 Qunyuan Zhang, Ph.D.
 Thomas B. Mooney, M.S.
```

EOS }

sub \_doc\_bugs {   \
     return \<\<EOS; For defects with any software in the genome namespace, contact\
  genome-dev ~at~ genome.wustl.edu. EOS }

sub \_doc\_credits {\
     return \<\<EOS, The MuSiC suite uses tabix, by Heng Li.  See http://samtools.sourceforge.net/tabix.shtml.

MuSiC depends on copies of data from the following databases, packaged in a form useable for quick analysis:

```
 * KEGG - http://www.genome.jp/kegg/
 * COSMIC - http://www.sanger.ac.uk/genetics/CGP/cosmic/
 * OMIM - http://www.ncbi.nlm.nih.gov/omim
 * Pfam - http://pfam.sanger.ac.uk/
 * SMART - http://smart.embl-heidelberg.de/
 * SUPERFAMILY - http://supfam.cs.bris.ac.uk/SUPERFAMILY/
 * PatternScan - http://www.expasy.ch/prosite/
```

EOS }

sub \_doc\_see\_also {\
     '[**genome**(1)](/genome/1.md)', }

1;