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gmt music pfam - Add Pfam annotation to a MAF file


This document describes gmt music pfam version 0.04 (2016-01-01 at 23:10:19)


gmt music pfam --maf-file=? --output-file=? --reference-build=?

... music pfam \
--maf-file myMAF.tsv \
--output-file myMAF.tsv.pfam


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:

Default value 'Build37' if not specified


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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