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PROGRAM:

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

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