---
name: "gmt-music-mutation-relation"
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-mutation-relation"
---

# gmt-music-mutation-relation(1p)

Identify relationships of mutation concurrency or mutual exclusivity in genes across cases.

## gmt music mutation-relation

## NAME

gmt music mutation-relation - Identify relationships of mutation concurrency or mutual exclusivity in genes across cases.

## VERSION

This document describes gmt music mutation-relation version 0.04 (2018-07-05 at 09:17:13)

## SYNOPSIS

gmt music mutation-relation --bam-list=? --maf-file=? --output-file=? \[--mutation-matrix-file=?\] \[--permutations=?\] \[--gene-list=?\] \[--skip-non-coding\] \[--skip-silent\]

```
 ... music mutation-relation \
        --maf-file /path/myMAF.tsv \
        --permutations 1000 \
        --output-file /path/mutation_relation.csv
```

## REQUIRED ARGUMENTS

- bam-list *Text*

  Tab delimited list of BAM files \[sample\_name, normal\_bam, tumor\_bam\] (See Description)

- maf-file *Text*

  List of mutations in MAF format

- output-file *Text*

  Results of mutation-relation tool

## OPTIONAL ARGUMENTS

- mutation-matrix-file *Text*

  Optionally store the sample-vs-gene matrix used during calculations.

- permutations *Number*

  Number of permutations used to determine P-values

  Default value '100' if not specified

- gene-list *Text*

  List of genes to test, typically SMGs. If unspecified, all genes in MAF are tested.

- 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 parses a list of mutations in MAF format and attempts to determine relationships among mutated genes. It employs a correlation test to see whether or not any two genes are mutated concurrently (positive correlation) or mutually exclusively (negative correlation). Because of the possibility of largely varying numbers of mutations present in different genes, P-values are calculated using restricted permutations that take into account the distribution of mutation counts among the samples. In the output file, 'pand' is the P-value for concurrent mutation events, and 'pexc' is the P-value for mutually exclusive mutation events.

## ARGUMENTS

- \--bam-list

  - Provide a file containing sample names and normal/tumor BAM locations for each. Use the tab- delimited format \[sample\_name normal\_bam tumor\_bam\] per line. This tool only needs sample\_name, so all other columns can be skipped. The sample\_name must be the same as the tumor sample names used in the MAF file (16th column, with the header Tumor\_Sample\_Barcode).

    ## AUTHORS

```
 Nathan D. Dees, Ph.D.
 Qunyuan Zhang, Ph.D.
```