gmt-music-play1p
Run the full suite of music tools sequentially.
Usage
gmt music
play
--bam-list=?
--roi-file=?
--reference-sequence=?
--output-dir=?
--maf-file=?
--pathway-file=?
[--numeric-clinical-data-file=?]
[--categorical-clinical-data-file=?]
[--mutation-matrix-file=?]
[--permutations=?]
[--normal-min-depth=?]
[--tumor-min-depth=?]
[--min-mapq=?]
[--show-skipped]
[--genes-to-ignore=?]
[--bmr=?]
[--max-proximity=?]
[--bmr-modifier-file=?]
[--numerical-data-test-method=?]
[--skip-low-mr-genes]
[--max-fdr=?]
[--genetic-data-type=?]
[--wu-annotation-headers]
[--bmr-groups=?]
[--separate-truncations]
[--merge-concurrent-muts]
[--skip-non-coding]
[--skip-silent]
[--min-mut-genes-per-path=?]
[--glm-model-file=?]
[--processors=?]
[--aa-range=?]
[--nuc-range=?]
[--reference-build=?]
[--show-known-hits]
[--glm-clinical-data-file=?]
[--use-maf-in-glm]
[--omimaa-dir=?]
[--cosmic-dir=?]
[--verbose]
[--clinical-correlation-matrix-file=?]
gmt music play
Version
This document describes gmt music play version 0.04 (2018-07-05 at 09:17:13)
Required arguments
bam-list Text
|
Tab delimited list of BAM files [sample_name normal_bam tumor_bam] |
|---|---|
roi-file Text
|
Tab delimited list of ROIs [chr start stop gene_name] |
reference-sequence Text
|
Path to reference sequence in FASTA format |
output-dir Text
|
Directory where output files and subdirectories will be written |
maf-file Text
|
List of mutations using TCGA MAF specifications v2.3 |
pathway-file Text
|
Tab-delimited file of pathway information |
Optional arguments
- numeric-clinical-data-file Text
-
Table of samples (y) vs. numeric clinical data category (x)
- categorical-clinical-data-file Text
-
Table of samples (y) vs. categorical clinical data category (x)
- mutation-matrix-file Text
-
Optionally store the sample-vs-gene matrix used during calculations.
- permutations Number
-
Number of permutations used to determine P-values
- normal-min-depth Integer
-
The minimum read depth to consider a Normal BAM base as covered
- tumor-min-depth Integer
-
The minimum read depth to consider a Tumor BAM base as covered
- min-mapq Integer
-
The minimum mapping quality of reads to consider towards read depth counts
- show-skipped Boolean
-
Report each skipped mutation, not just how many
Default value 'false' (--noshow-skipped) if not specified
- noshow-skipped Boolean
-
Make show-skipped 'false'
- genes-to-ignore Text
-
Comma-delimited list of genes to ignore for background mutation rates
- bmr Number
-
Background mutation rate in the targeted regions
- max-proximity Text
-
Maximum AA distance between 2 mutations
- bmr-modifier-file Text
-
Tab delimited list of values per gene that modify BMR before testing [gene_name bmr_modifier]
- numerical-data-test-method Text
-
Either 'cor' for Pearson Correlation or 'wilcox' for the Wilcoxon Rank-Sum Test for numerical clinical data.
Default value 'cor' if not specified
- skip-low-mr-genes Boolean
-
Skip testing genes with MRs lower than the background MR
Default value 'true' if not specified
- noskip-low-mr-genes Boolean
-
Make skip-low-mr-genes 'false'
- max-fdr Number
-
The maximum allowed false discovery rate for a gene to be considered an SMG
Default value '0.2' if not specified
- genetic-data-type Text
-
Data in matrix file must be either "gene" or "variant" type data
- wu-annotation-headers Boolean
-
Use this to default to wustl annotation format headers
- nowu-annotation-headers Boolean
-
Make wu-annotation-headers 'false'
- bmr-groups Integer
-
Number of clusters of samples with comparable BMRs
Default value '1' if not specified
- separate-truncations Boolean
-
Group truncational mutations as a separate category
Default value 'false' (--noseparate-truncations) if not specified
- noseparate-truncations Boolean
-
Make separate-truncations 'false'
- merge-concurrent-muts Boolean
-
Multiple mutations of a gene in the same sample are treated as 1
Default value 'false' (--nomerge-concurrent-muts) if not specified
- nomerge-concurrent-muts Boolean
-
Make merge-concurrent-muts 'false'
- 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'
- min-mut-genes-per-path Integer
-
Pathways with fewer mutated genes than this will be ignored
Default value '1' if not specified
- glm-model-file Text
-
File outlining the type of model, response variable, covariants, etc. for the GLM analysis. (See DESCRIPTION).
- processors Integer
-
Number of processors to use in SMG (requires 'foreach' and 'doMC' R packages)
Default value '1' if not specified
- aa-range Integer
-
Set how close a 'near' match is when searching for amino acid near hits
Default value '2' if not specified
- nuc-range Integer
-
Set how close a 'near' match is when searching for nucleotide position near hits
Default value '5' if not specified
- reference-build Text
-
Put either "Build36" or "Build37"
Default value 'Build37' if not specified
- show-known-hits Boolean
-
When a finding is novel, show known AA in that gene
Default value 'true' if not specified
- noshow-known-hits Boolean
-
Make show-known-hits 'false'
- glm-clinical-data-file Text
-
Clinical traits, mutational profiles, other mixed clinical data (See DESCRIPTION).
- use-maf-in-glm Boolean
-
Set this flag to use the variant matrix created from the MAF file as variant input to GLM analysis.
Default value 'false' (--nouse-maf-in-glm) if not specified
- nouse-maf-in-glm Boolean
-
Make use-maf-in-glm 'false'
- omimaa-dir Path
-
omim amino acid mutation database folder
- cosmic-dir Path
-
cosmic amino acid mutation database folder
- verbose Boolean
-
turn on to display larger working output
Default value 'true' if not specified
- noverbose Boolean
-
Make verbose 'false'
- clinical-correlation-matrix-file Text
-
Optionally store the sample-vs-gene matrix used internally during calculations.
Overview
This command can be used to run all of the MuSiC analysis tools on a set of data. Please see the individual tools for further description of the parameters.
Credits
Please see the credits for genome-music(1).
Releases
3 releases since Debian 8 (Jessie); the text changed 2 times.