gmt music pfam

NAME

       gmt music pfam - Add Pfam annotation to a MAF file

VERSION

       This document describes gmt music pfam version 0.04 (2013-05-25 at 17:45:02)

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)