.\" Automatically generated by Pod::Man 4.09 (Pod::Simple 3.35)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.if !\nF .nr F 0
.if \nF>0 \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    if !\nF==2 \{\
.        nr % 0
.        nr F 2
.    \}
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "GENOME-MUSIC-COSMIC-OMIM 1p"
.TH GENOME-MUSIC-COSMIC-OMIM 1p "2018-07-05" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "genome music cosmic-omim"
.IX Header "genome music cosmic-omim"
.SH "NAME"
genome music cosmic\-omim \- Compare the amino acid changes of supplied mutations to COSMIC and OMIM databases.
.SH "VERSION"
.IX Header "VERSION"
This document describes genome music cosmic-omim (2018\-07\-05 at 09:17:13)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
genome music cosmic-omim \-\-maf\-file=? \-\-output\-file=? \-\-reference\-build=? [\-\-omimaa\-dir=?] [\-\-cosmic\-dir=?] [\-\-verbose] [\-\-wu\-annotation\-headers] [\-\-aa\-range=?] [\-\-nuc\-range=?] [\-\-show\-known\-hits]
.PP
.Vb 4
\& ... music cosmic\-omim \e
\&        \-\-maf\-file input_dir/myMAF.tsv \e
\&        \-\-output\-file output_dir/myMAF_output.tsv \e
\&        \-\-no\-verbose
\&
\& ... music cosmic\-omim \e
\&        \-\-maf\-file input_dir/myMAF.tsv \e
\&        \-\-output\-file output_dir/myMAF_output.tsv \e
\&        \-\-omimaa\-dir omim_dir/ \e
\&        \-\-cosmic\-dir cosmic_dir/ \e
\&        \-\-no\-verbose
.Ve
.SH "REQUIRED ARGUMENTS"
.IX Header "REQUIRED ARGUMENTS"
.IP "maf-file  \fIPath\fR" 4
.IX Item "maf-file Path"
list of annotated mutations in \s-1MAF\s0 format (or any file with MAF+annotation headers)
.IP "output-file  \fIPath\fR" 4
.IX Item "output-file Path"
Output file contains the input file with two columns appended to the end, corresponding to cosmic and omim mutation comparisons, respectively
.IP "reference-build  \fIText\fR" 4
.IX Item "reference-build Text"
Put either \*(L"Build36\*(R" or \*(L"Build37\*(R"
.Sp
Default value 'Build37' if not specified
.SH "OPTIONAL ARGUMENTS"
.IX Header "OPTIONAL ARGUMENTS"
.IP "omimaa-dir  \fIPath\fR" 4
.IX Item "omimaa-dir Path"
omim amino acid mutation database folder
.IP "cosmic-dir  \fIPath\fR" 4
.IX Item "cosmic-dir Path"
cosmic amino acid mutation database folder
.IP "verbose  \fIBoolean\fR" 4
.IX Item "verbose Boolean"
Use this to display the larger working output
.Sp
Default value 'false' (\-\-noverbose) if not specified
.IP "noverbose  \fIBoolean\fR" 4
.IX Item "noverbose Boolean"
Make verbose 'false'
.IP "wu-annotation-headers  \fIBoolean\fR" 4
.IX Item "wu-annotation-headers Boolean"
Use this if input \s-1MAF\s0 contains \s-1WUSTL\s0 annotation format headers
.Sp
Default value 'false' (\-\-nowu\-annotation\-headers) if not specified
.IP "nowu-annotation-headers  \fIBoolean\fR" 4
.IX Item "nowu-annotation-headers Boolean"
Make wu-annotation-headers 'false'
.IP "aa-range  \fIInteger\fR" 4
.IX Item "aa-range Integer"
Set how close a 'near' match is when searching for amino acid near hits
.Sp
Default value '2' if not specified
.IP "nuc-range  \fIInteger\fR" 4
.IX Item "nuc-range Integer"
Set how close a 'near' match is when searching for nucleotide position near hits
.Sp
Default value '5' if not specified
.IP "show-known-hits  \fIBoolean\fR" 4
.IX Item "show-known-hits Boolean"
When a finding is novel, show known \s-1AA\s0 in that gene
.Sp
Default value 'true' if not specified
.IP "noshow-known-hits  \fIBoolean\fR" 4
.IX Item "noshow-known-hits Boolean"
Make show-known-hits 'false'
.SH "DESCRIPTION"
.IX Header "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 \s-1OMIM\s0 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 \*(L"near proximity\*(R", where \*(L"near proximity\*(R" is currently defined as a linear \s-1DNA\s0 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 \*(L"novel\*(R" with respect to that database.
.PP
The output of this script returns each row the original input \s-1MAF\s0 file with two columns appended to the end of each, one column for each of the databases. Also included is a \s-1STDOUT\s0 printout of a summary of what was found in the input \s-1MAF.\s0 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 \s-1MAF\s0 problems. The Omim and Cosmic directories must point to the output of the downloader, named appropriately, as they don't recognize the \s-1OMIM\s0 database in the raw download format.
.PP
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.
.PP
In addition to the standard version 2.3 \s-1MAF\s0 headers, there needs to be 3 columns appended. These
column headers in the \s-1MAF\s0 must have these names in the header in order for the tool to find them:
   transcript_name \- the transcript name, such as \s-1NM_000028\s0
 amino_acid_change \- the amino acid change, such as p.R290H
        c_position \- the nucleotide position changed, such as c.869
.SH "LICENSE"
.IX Header "LICENSE"
Copyright (C) 2010\-2011 Washington University in St. Louis.
.PP
It is released under the Lesser \s-1GNU\s0 Public License (\s-1LGPL\s0) version 3.  See the 
associated \s-1LICENSE\s0 file in this distribution.
.SH "AUTHORS"
.IX Header "AUTHORS"
.Vb 4
\& Brian Dunford\-Shore
\& David Larson, Ph.D.
\& Michael C. Wendl, Ph.D.
\& William Schierding, M.S.
.Ve
.SH "CREDITS"
.IX Header "CREDITS"
This tool depends on copies of data from the following databases, packaged in a form useable for quick analysis:
.PP
.Vb 2
\& * COSMIC \- http://www.sanger.ac.uk/genetics/CGP/cosmic/
\& * OMIM \- http://www.ncbi.nlm.nih.gov/omim
.Ve
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fBgenome-music\fR(1), \fBgenome\fR(1)