genome music proximity
NAME
genome music proximity - Perform a proximity analysis on a list of mutations.
VERSION
This document describes genome music proximity version 0.0401 (2014-02-13 at 08:01:07)
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.