---
name: "genome-music-path-scan"
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/genome-music-path-scan"
---

# genome-music-path-scan(1p)

Find significantly mutated pathways in a cohort given a list of somatic mutations.

## genome music path-scan

## NAME

genome music path-scan - Find significantly mutated pathways in a cohort given a list of somatic mutations.

## VERSION

This document describes genome music path-scan version 0.04 (2018-07-05 at 09:17:13)

## SYNOPSIS

genome music path-scan --gene-covg-dir=? --bam-list=? --pathway-file=? --maf-file=? --output-file=? \[--bmr=?\] \[--genes-to-ignore=?\] \[--min-mut-genes-per-path=?\] \[--skip-non-coding\] \[--skip-silent\]

```
 ... music path-scan \
        --bam-list input_dir/bam_file_list \
        --gene-covg-dir output_dir/gene_covgs/ \
        --maf-file input_dir/myMAF.tsv \
        --output-file output_dir/sm_pathways \
        --pathway-file input_dir/pathway_dbs/KEGG.txt \
        --bmr 8.7E-07
```

## REQUIRED ARGUMENTS

- gene-covg-dir *Text*

  Directory containing per-gene coverage files (Created using music bmr calc-covg)

- bam-list *Text*

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

- pathway-file *Text*

  Tab-delimited file of pathway information (See Description)

- maf-file *Text*

  List of mutations using TCGA MAF specifications v2.3

- output-file *Text*

  Output file that will list the significant pathways and their p-values

## OPTIONAL ARGUMENTS

- bmr *Number*

  Background mutation rate in the targeted regions

  Default value '1e-06' if not specified

- genes-to-ignore *Text*

  Comma-delimited list of genes whose mutations should be ignored

- min-mut-genes-per-path *Number*

  Pathways with fewer mutated genes than this, will be ignored

  Default value '1' 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

Only the following four columns in the MAF are used. All other columns may be left blank.

```
 Col 1: Hugo_Symbol (Need not be HUGO, but must match gene names used in the pathway file)
 Col 2: Entrez_Gene_Id (Matching Entrez ID trump gene name matches between pathway file and MAF)
 Col 9: Variant_Classification
 Col 16: Tumor_Sample_Barcode (Must match the name in sample-list, or contain it as a substring)
```

The Entrez\_Gene\_Id can also be left blank (or set to 0), but it is highly recommended, in case genes are named differently in the pathway file and the MAF file.

## ARGUMENTS

- \--pathway-file

  - This is a tab-delimited file prepared from a pathway database (such as KEGG), with the columns: \[path\_id, path\_name, class, gene\_line, diseases, drugs, description\] The latter three columns are optional (but are available on KEGG). The gene\_line contains the "entrez\_id:gene\_name" of all genes involved in this pathway, each separated by a "\|" symbol.

    For example, a line in the pathway-file would look like:

    ```
      hsa00061    Fatty acid biosynthesis    Lipid Metabolism    31:ACACA|32:ACACB|27349:MCAT|2194:FASN|54995:OXSM|55301:OLAH
    ```

    Ensure that the gene names and entrez IDs used match those used in the MAF file. Entrez IDs are not mandatory (use a 0 if Entrez ID unknown). But if a gene name in the MAF does not match any gene name in this file, the entrez IDs are used to find a match (unless it's a 0).

- \--gene-covg-dir

  - This is usually the gene\_covgs subdirectory created when you run "music bmr calc-covg". It should contain files for each sample that report per-gene covered base counts.

    - \--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).

    - \--bmr

  - The overall background mutation rate. This can be calculated using "music bmr calc-bmr".

    - \--genes-to-ignore

  - A comma-delimited list of genes to ignore from the MAF file. This is useful when there are recurrently mutated genes like TP53 which might mask the significance of other genes.

    ## AUTHORS

```
 Michael Wendl, Ph.D.
```

## CREDITS

This module uses reformatted copies of data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database:

```
 * KEGG - http://www.genome.jp/kegg/
```