Provided by: libgenome-model-tools-music-perl_0.04-3_all 
gmt music pfam
NAME
gmt music pfam - Add Pfam annotation to a MAF file
VERSION
This document describes gmt music pfam version 0.04 (2016-01-01 at 23:10:19)
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)
perl v5.22.1 2016-01-01 GMT-MUSIC-PFAM(1p)