# genotype

## Version of tools in docker image (/container/Dockerfile)

| Tool                 | Version | Location                                   |
| -------------------- | ------- | ------------------------------------------ |
| biometrics\_genotype | 0.2.15  | <https://github.com/msk-access/biometrics> |

## CWL

* CWL specification 1.0
* Use example\_inputs.json to see the inputs to the cwl
* Example Command using [toil](https://toil.readthedocs.io):

```bash
    > toil-cwl-runner biometrics_genotype.cwl example_inputs.json
```

```bash
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/biometrics_genotype.cwl /path/to/example_inputs.json

#Using toil-cwl-runner
> mkdir tool_toil_log
> toil-cwl-runner --singularity --logFile /path/to/tool_toil_log/cwltoil.log  --jobStore /path/to/tool_jobStore --batchSystem lsf --workDir /path/to/tool_toil_log --outdir . --writeLogs /path/to/tool_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/biometrics_genotype.cwl /path/to/example_inputs.json > tool_toil.stdout 2> tool_toil.stderr &
```

### Usage

```bash
> toil-cwl-runner biometrics_genotype.cwl -h
usage: biometrics_genotype/0.2.15/biometrics_genotype.cwl [-h] --input INPUT [--database DATABASE]
                                                          [--discordance_threshold DISCORDANCE_THRESHOLD]
                                                          [--prefix PREFIX] [--plot] [--json]
                                                          [--no_db_comparison] [--het HET][--threads THREADS]
                                                          [job_order]

positional arguments:
  job_order             Job input json file

optional arguments:
  -h, --help            show this help message and exit
  --input INPUT         Can be one of three types: (1) path to a CSV file containing sample information
                        (one per line). For example:
                        sample_name,sample_bam,sample_type,sample_sex,sample_group. (2) Path to a '*.pk'
                        file that was produced by the 'extract' tool. (3) Name of the sample to analyze;
                        this assumes there is a file named '{sample_name}.pk' in your database directory.
                        Can be specified more than once.
  --database DATABASE   Directory to store the intermediate files after running the extraction step.
  --discordance_threshold DISCORDANCE_THRESHOLD
                        Discordance values less than this are regarded as matching samples. (default:
                        0.05)
  --prefix PREFIX       Output file prefix.
  --plot                Also output plots of the data.
  --json                Also output data in JSON format.
  --no_db_comparison    Do not compare the sample(s) you provided to all samples in the database, only
                        compare them with each other.
  --het                 Include Hetrozygous sites along with homozygous sites when calculating discordant rate, helps specifically in cases where there are less than 100 total number of sites
  --threads THREADS     Number of threads to use.
```


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