genome-music-survivalp - Online in the Cloud

PROGRAM:

NAME

genome music survival - Create survival plots and P-values for clinical and mutational
phenotypes.

VERSION

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

SYNOPSIS

genome music survival --bam-list=? --output-dir=? [--maf-file=?] [--skip-silent]
[--genetic-data-type=?] [--numeric-clinical-data-file=?]
[--categorical-clinical-data-file=?] [--glm-clinical-data-file=?]
[--phenotypes-to-include=?] [--legend-placement=?] [--skip-non-coding]

... music survival
--bam-list /path/myBamList.tsv
--maf-file /path/myMAF.tsv
--numeric-clinical-data-file /path/myNumericData.tsv
--categorical-clinical-data-file /path/myClassData.tsv
--output-dir /path/output_directory

... music survival
--bam-list /path/myBamList.tsv
--maf-file /path/myMAF.tsv
--glm-clinical-data-file /path/myGLMClinicalData.tsv
--output-dir /path/output_directory

... music survival
--bam-list /path/myBamList.tsv
--maf-file /path/myMAF.tsv
--genetic-data-type 'gene'
--glm-clinical-data-file /path/myGlmClinicalData.tsv
--phenotypes-to-include 'Race,Gender,TP53'
--output-dir /path/output_directory

REQUIRED ARGUMENTS

bam-list Text
List of sample names to be included in the analysis. (See Description)

output-dir Text
Directory where output files will be written

OPTIONAL ARGUMENTS

maf-file Text
List of mutations in MAF format

skip-silent Boolean
Skip silent mutations from the provided MAF file

Default value 'true' if not specified

noskip-silent Boolean
Make skip-silent 'false'

genetic-data-type Text
Correlate clinical data to "gene" or "variant" level data

Default value 'gene' 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)

glm-clinical-data-file Text
Clinical traits, mutational profiles, other mixed clinical data (See DESCRIPTION).

phenotypes-to-include Text
Include only these genes and/or phenotypes in the anlaysis. (COMMA-DELIMITED)

legend-placement Text
Choose one of 'bottomleft', 'topleft', 'topright', or 'bottomright'.

Default value 'bottomleft' 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'

DESCRIPTION

This command performs survival analysis and plots survival curves for mutational data, as
well as any clinical traits of interest as specified via the --phenotypes-to-include input
parameter. The analyses performed include the Kaplan-Meier estimator followed by the Cox
Proportional Hazards model. Outputs for each gene/clinical trait analyzed include survival
curves, a hazard ratio (with confidence intervals), and P-values and FDRs describing the
significance of the difference between survivors and non-survivors.

All clinical data files are searched for the required (case insensitive) "vital_status"
and "days_to_last_followup" columns which are paired to phenotypes via sample IDs for the
survival analysis. The first column of all clinical data files MUST contain the sample
IDs, same as in other MuSiC tools. By default, analysis is performed on every gene present
in the MAF. Optionally, the analysis may be limited to only specific genes by listing them
(comma delimited) after the --phenotypes-to-include input parameter. Survival analysis may
also be performed on other columns in the clinical data file by adding the column headers
to the list of entries specified after the --phenotypes-to-include input parameter.

Here are some general guildelines for creating clinical data input files:

· Headers are required.

· The first column of each clinical data file must contain sample IDs which match those
in both the --bam-list and the MAF variant list (in the MAF, this is the
Tumor_Sample_Barcode column, specifically).

· In at least one of the clinical data files input, columns with headers "vital_status"
and "days_to_last_followup" (case insensitive) must exist. "vital_status" must be
delineated by 1's and 0's, where 0 denotes 'living', and 1 denotes 'deceased'.

Note that all input files must be tab-separated.

ARGUMENTS

--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).

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