4. Prepare Synopsis¶

The ./metro executable is composed of several inter-related sub commands. Please see ./metro -h for all available options. The synopsis for the sub command prepare shows its parameters and their usage. Optional parameters are shown in square brackets.

$ ./metro prepare [-h] --mafFiles MAFFILES \
                      --outputdir OUTPUTdir \
                      --outputprefix OUTPUTprefix \
                      [--vafFilter VAFFILTER] \
                      [--passFilter PASSFILTER] \
                      [--impactFilter IMPACTFILTER]

This part of the documentation describes options and concepts for ./metro prepare sub command in more detail. With minimal configuration, the prepare sub command enables you to create filtered MAF files for the metro run pipeline.

4.1 Required Arguments¶

Each of the following arguments are required. Failure to provide a required argument will result in a non-zero exit-code. --mafFiles MAFFILES [MAFFILES ...]

Input MAF-like file(s) to process.
type: file

Input VCF file(s) in MAF format. Provide a minimum of two files, separated by a comma.

Example: --mafFiles data/test1.maf,data/test2.maf

--outputdir OUTPUTDIR

Path to an output directory.
type: path

This location is where the metro will create all of its output files, also known as the pipeline's working directory. If the provided output directory does not exist, it will be created automatically.

Example: --outputdir /scratch/$USER/RNA_hg38

--outputprefix OUTPUTPREFIX

Output file prefix.
type: prefix

Prefix for sample output files.

Example: --outputprefix test

4.2 Optional Arguments¶

Each of the following arguments are optional and do not need to be provided. Default values listed in each example will be used, if value not provided.

-h, --help

Display Help.
type: boolean

Shows command's synopsis, help message, and an example command

Example: --help

--vafFilter VAFFilter

Filter for VAF values.
type: numeric

Minimum value for average VAF, calculated as t_alt_count/t_depth, to be included.

Example: --vafFilter 0.2

--passFilter PASSFILTER

Filter for PASS values.
type: numeric

Minimum number of input files with a filter rating of "PASS", to be included.

Example: --passFilter 2

--impactFilter IMPACTFILTER

Filter for IMPACT values.
type: numeric

Minimum number of input files with an IMPACT rating of "MODERATE" or "HIGH", to be included.

Example: --impactFilter 2

4.3 Example¶

Filter MAF files in preparation of metro run.

# login and load interactive session, as described in Getting Started

### Github
module purge
module load python/4.5

## Docker
singularity shell --bind /data/$USER,/usr/local/apps/cufflinks/2.2.1 docker://nciccbr/metro_v1.4:latest

## Command
 ./metro prepare \
            --mafFiles /scratch/$USER/METRO/data/*.maf \
            --outputDir /scratch/$USER/METRO \
            --outprefix test \
            --vafFilter 0.2 \
            --passFilter 2 \
            --impactFilter 2