gmt music path-scan¶
NAME¶
gmt music path-scan - Find signifcantly mutated pathways in a cohort given a
list of somatic mutations.
VERSION¶
This document describes gmt music path-scan version 0.04 (2013-05-14 at
16:03:05)
SYNOPSIS¶
gmt 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
- skip-silent Boolean
- Skip silent mutations from the provided MAF file
Default value 'true' if not specified
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/
