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GENOME-MUSIC-PATH-SCAN(1p) User Contributed Perl Documentation GENOME-MUSIC-PATH-SCAN(1p)

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

Directory containing per-gene coverage files (Created using music bmr calc-covg)
Tab delimited list of BAM files [sample_name, normal_bam, tumor_bam] (See Description)
Tab-delimited file of pathway information (See Description)
List of mutations using TCGA MAF specifications v2.3
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

Comma-delimited list of genes whose mutations should be ignored
Pathways with fewer mutated genes than this, will be ignored

Default value '1' if not specified

Skip non-coding mutations from the provided MAF file

Default value 'true' if not specified

Make skip-non-coding 'false'
Skip silent mutations from the provided MAF file

Default value 'true' if not specified

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

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).

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/
2018-07-05 perl v5.26.2