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 (2013-05-14 at 16:03:04)

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.