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gmt music cosmic-omim

NAME

       gmt music cosmic-omim - Compare the amino acid changes of supplied mutations to COSMIC and OMIM
       databases.

VERSION

       This document describes gmt music cosmic-omim (2016-01-01 at 23:10:19)

SYNOPSIS

       gmt music cosmic-omim --maf-file=? --output-file=? --reference-build=? [--omimaa-dir=?] [--cosmic-dir=?]
       [--verbose] [--wu-annotation-headers] [--aa-range=?] [--nuc-range=?] [--show-known-hits]

        ... music cosmic-omim \
               --maf-file input_dir/myMAF.tsv \
               --output-file output_dir/myMAF_output.tsv \
               --no-verbose

        ... music cosmic-omim \
               --maf-file input_dir/myMAF.tsv \
               --output-file output_dir/myMAF_output.tsv \
               --omimaa-dir omim_dir/ \
               --cosmic-dir cosmic_dir/ \
               --no-verbose

REQUIRED ARGUMENTS

       maf-file  Path
           list of annotated mutations in MAF format (or any file with MAF+annotation headers)

       output-file  Path
           Output file contains the input file with two columns appended to the end, corresponding to cosmic and
           omim mutation comparisons, respectively

       reference-build  Text
           Put either "Build36" or "Build37"

           Default value 'Build37' if not specified

OPTIONAL ARGUMENTS

       omimaa-dir  Path
           omim amino acid mutation database folder

       cosmic-dir  Path
           cosmic amino acid mutation database folder

       verbose  Boolean
           Use this to display the larger working output

           Default value 'false' (--noverbose) if not specified

       noverbose  Boolean
           Make verbose 'false'

       wu-annotation-headers  Boolean
           Use this if input MAF contains WUSTL annotation format headers

           Default value 'false' (--nowu-annotation-headers) if not specified

       nowu-annotation-headers  Boolean
           Make wu-annotation-headers 'false'

       aa-range  Integer
           Set how close a 'near' match is when searching for amino acid near hits

           Default value '2' if not specified

       nuc-range  Integer
           Set how close a 'near' match is when searching for nucleotide position near hits

           Default value '5' if not specified

       show-known-hits  Boolean
           When a finding is novel, show known AA in that gene

           Default value 'true' if not specified

       noshow-known-hits  Boolean
           Make show-known-hits 'false'

DESCRIPTION

This tool looks at the amino acid changes for the given set of mutations and compares the genomic
coordinates as well as the affected amino acid to the coordinates and amino acids of all cancer-specific
mutations listed in the Cosmic and OMIM databases. The database files are specially prepared for this
task and provided with the MuSiC suite. The tool reports various types of matches, including matches
within "near proximity", where "near proximity" is currently defined as a linear DNA distance of 5 bases
or 2 amino acids. (This type of matching helps to account for the possibility of subtle differences in
reported positions for variants due to differences in transcript definitions or other things of this
nature.) Any site without a match in a particular databases is reported as "novel" with respect to that
database.

The output of this script returns each row the original input MAF file with two columns appended to the
end of each, one column for each of the databases. Also included is a STDOUT printout of a summary of
what was found in the input MAF. Neither output can be suppressed in the current version. The --verbose
option is used to display working notes that are useful for various purposes in debugging potential MAF
problems. The Omim and Cosmic directories must point to the output of the downloader, named
appropriately, as they don't recognize the OMIM database in the raw download format.

This tool only compares build 36 or build 37 coordinates that are specified in Cosmic to the coordinates
in your maf file. This is a weakness of the Cosmic database (not all position entries are currently
available for both builds) that is out of our control.

In addition to the standard version 2.3 MAF headers, there needs to be 3 columns appended. These column
headers in the MAF must have these names in the header in order for the tool to find them:
transcript_name - the transcript name, such as NM_000028 amino_acid_change - the amino acid change,
such as p.R290H
c_position - the nucleotide position changed, such as c.869

LICENSE

       Copyright (C) 2010-2011 Washington University in St. Louis.

       It is released under the Lesser GNU Public License (LGPL) version 3.  See the associated LICENSE file  in
       this distribution.

AUTHORS

        Brian Dunford-Shore
        David Larson, Ph.D.
        Michael C. Wendl, Ph.D.
        William Schierding, M.S.

CREDITS

       This  tool  depends  on copies of data from the following databases, packaged in a form useable for quick
       analysis:

        * COSMIC - http://www.sanger.ac.uk/genetics/CGP/cosmic/
        * OMIM - http://www.ncbi.nlm.nih.gov/omim