---
name: "gmt-music-pfam"
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/gmt-music-pfam"
---

# gmt-music-pfam(1p)

Add Pfam annotation to a MAF file

## gmt music pfam

## NAME

gmt music pfam - Add Pfam annotation to a MAF file

## VERSION

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

## SYNOPSIS

gmt music pfam --maf-file=? --output-file=? --reference-build=?

```
 ... music pfam \
        --maf-file myMAF.tsv \
        --output-file myMAF.tsv.pfam
```

## REQUIRED ARGUMENTS

- maf-file *Text*

  List of mutations using TCGA MAF specification v2.3

- output-file *Text*

  Output MAF file with an extra column that reports Pfam annotation domains

- reference-build *Text*

  Options are 'Build36' or 'Build37'. This parameter ensures appropriate annotation of domains valid values:\
    Build36\
    Build37

  Default value 'Build37' if not specified

## DESCRIPTION

This command adds Pfam Domains to a column at the end of a MAF file.

This tool takes a MAF file, determines the location of each variant therein, and then uses a fast-lookup to retrieve all of the Pfam annotation domains that the variant crosses. A column is appended to the end of the input MAF file called "Pfam\_Annotation\_Domains" where the results are listed. "NA" is listed if no Pfam domains are found.

## LICENSE

Copyright (C) 2010-2011 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.

## AUTHORS

```
 Nathan D. Dees, Ph.D.
```

## CREDITS

This tool uses tabix, by Heng Li.  See http://samtools.sourceforge.net/tabix.shtml.

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

```
 * 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/
```

## SEE ALSO

**genome-music**(1), [**genome**(1)](/genome/1.md)