gmt-music-pfam1p

Usage

gmt music pfam

Version

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

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

Overview

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.

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/