genome-music-galaxyp - Online in the Cloud

PROGRAM:

NAME

genome music galaxy - Run the full suite of MuSiC tools sequentially.

VERSION

This document describes genome music galaxy version 0.04 (2016-01-01 at 23:10:18)

SYNOPSIS

genome music galaxy [--output-dir=?] --bam-list=? --output-bundle=? --roi-file=?
--reference-sequence=? --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=?]

This tool takes as parameters all the information required to run the individual tools. An
example usage is:

... music play \
--bam-list input/bams_to_analyze.txt \
--numeric-clinical-data-file input/numeric_clinical_data.csv \
--maf-file input/myMAF.tsv \
--output-dir play_output_dir \
--pathway-file input/pathway_db \
--reference-sequence input/refseq/all_sequences.fa \
--roi-file input/all_coding_regions.bed \
--genetic-data-type gene

REQUIRED ARGUMENTS

bam-list Text
Tab delimited list of BAM files [sample_name normal_bam tumor_bam]

output-bundle Text
Location where Galaxy would like the bundle of Music outputs to be saved

roi-file Text
Tab delimited list of ROIs [chr start stop gene_name]

reference-sequence Text
Path to reference sequence in FASTA format

maf-file Text
List of mutations using TCGA MAF specifications v2.3

pathway-file Text
Tab-delimited file of pathway information

OPTIONAL ARGUMENTS

output-dir
Directory where output files and subdirectories will be written

Default value '' if not specified

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.

DESCRIPTION

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.

AUTHORS

Thomas B. Mooney, M.S.

CREDITS

Please see the credits for genome-music(1).

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