GENOME-MUSIC-PROXIMITY

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 (2016−01−01 at 23:10:18)

SYNOPSIS

genome music proximity −−maf−file=? −−output−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-file Text

TODO

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

noskip-non-coding Boolean

Make skip-non-coding ’false’

skip-silent Boolean

Skip silent mutations from the provided MAF file

Default value ’true’ if not specified

noskip-silent Boolean

Make skip-silent ’false’

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.