genome music proximity

NAME

       genome music proximity - Perform a proximity analysis on a list of mutations.

VERSION

       This document describes genome music proximity version 0.04 (2013-05-25 at 17:45:01)

SYNOPSIS

       genome music proximity --maf-file=? --output-dir=? [--max-proximity=?] [--skip-non-coding]
       [--skip-silent]

        ... music proximity \
               --maf-file input_dir/myMAF.tsv \
               --output-dir output_dir/ \
               --max-proximity 15

REQUIRED ARGUMENTS

       maf-file  Text
           List of mutations using TCGA MAF specifications v2.3

       output-dir  Text
           Directory where output files will be written

OPTIONAL ARGUMENTS

       max-proximity  Text
           Maximum allowed AA distance between 2 mutations

           Default value '7' if not specified

       skip-non-coding  Boolean
           Skip non-coding mutations from the provided MAF file

           Default value 'true' if not specified

       skip-silent  Boolean
           Skip silent mutations from the provided MAF file

           Default value 'true' if not specified

DESCRIPTION

       This  module  first  calculates  the  amino  acid  position  of  each mutation in the MAF file within its
       respective transcript. Then, for each mutation, two  values  are  calculated:  1)  the  number  of  other
       mutations on the same transcript within the proximity limit set by the max-proximity input parameter, and
       2)  the  distance  to  the  closest  other mutation in this nearby set. Only mutations which have another
       mutation within close proximity are reported in the output-file.

       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

       The  output  is generated with the folowing column headers: Mutations_Within_Proximity, Nearest_Mutation,
       Gene, Transcript, Affected_Amino_Acid(s), Chr, Start, Stop, Ref_Allele, Var_Allele, Sample

AUTHORS

        Nathan D. Dees, Ph.D.
        Dan Koboldt, M.S.
        Cyriac Kandoth, Ph.D.

perl v5.14.2                                       2013-05-25                         GENOME-MUSIC-PROXIMITY(1p)