Add pfam annotation to a maf file
This document describes genome music pfam version 0.04 (2013-05-14 at 16:03:04)
genome music pfam --maf-file=? --output-file=? --reference-build=?
... music pfam \
--maf-file myMAF.tsv \
--output-file myMAF.tsv.pfam
List of mutations using \s-1TCGA\s0 \s-1MAF\s0 specification v2.3
Output \s-1MAF\s0 file with an extra column that reports Pfam annotation domains
Options are 'Build36' or 'Build37'. This parameter ensures appropriate annotation of domains valid values: Build36 Build37 Default value 'Build37' if not specified
This command adds Pfam Domains to a column at the end of a \s-1MAF\s0 file.
This tool takes a \s-1MAF\s0 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 \s-1MAF\s0 file called \*(L"Pfam_Annotation_Domains\*(R" where the results are listed. \*(L"\s-1NA\s0\*(R" is listed if no Pfam domains are found.
Copyright (C) 2010-2011 Washington University in St. Louis.
It is released under the Lesser \s-1GNU\s0 Public License (\s-1LGPL\s0) version 3. See the associated \s-1LICENSE\s0 file in this distribution.
Nathan D. Dees, Ph.D.
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/
genome-music(1), genome(1)