---
name: "gmt-music-proximity"
section: "1p"
platform: "linux"
package: "libgenome-model-tools-music-perl"
version: "0.04-4"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/gmt-music-proximity"
---

# gmt-music-proximity(1p)

Perform a proximity analysis on a list of mutations.

## 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 (2018-07-05 at 09:17:13)

## SYNOPSIS

gmt 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 following 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.
```