genome-music-proximity1p
Perform a proximity analysis on a list of mutations.
Usage
genome music
proximity
--maf-file=?
--output-file=?
--output-dir=?
[--max-proximity=?]
[--skip-non-coding]
[--skip-silent]
genome music proximity
Version
This document describes genome music proximity version 0.04 (2018-07-05 at 09:17:13)
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'
Overview
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 following column headers: Mutations_Within_Proximity, Nearest_Mutation, Gene, Transcript, Affected_Amino_Acid(s), Chr, Start, Stop, Ref_Allele, Var_Allele, Sample
Releases
3 releases since Debian 8 (Jessie); the text changed 2 times.