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

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/