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 (2013-05-25 at 17:45:01)

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

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

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

       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

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

SEE ALSO

       genome-music(1), genome(1)