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This is the command gmt-music-pfamp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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.

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