gmt music proximity

NAME

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

VERSION

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

SYNOPSIS

       gmt 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.