# v1.8.2

To run VarDistJava in single sample mode vardict\_workflow\_single\_sample.cwl should be run. vardict\_workflow\_single\_sample.cwl will run 3 workflows to implement the example command in the original documentations as explained here: <https://github.com/AstraZeneca-NGS/VarDictJava#single-sample-mode>

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

| Tool                       | Version   | Location                                                             |
| -------------------------- | --------- | -------------------------------------------------------------------- |
| ubuntu base image (alpine) | 3.8       | -                                                                    |
| vardict                    | 1.8.2     | <https://github.com/AstraZeneca-NGS/VarDictJava/releases/tag/v1.8.2> |
| perl                       | 5.26.2-r1 | <https://pkgs.alpinelinux.org/package/edge/main/aarch64/perl>        |
| r                          | 3.5.1     | <https://pkgs.alpinelinux.org/package/edge/community/x86/R>          |

## CWL

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

```bash
    > toil-cwl-runner vardict_single_sample.cwl example_inputs.yaml
```

**If at MSK, using the JUNO cluster you can use the following command**

```bash
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/vardict_1.8.2/vardict_single_sample.cwl /path/to/inputs.yaml

#Using Toil-cwl-runner
toil-cwl-runner --singularity vardict_single_sample.cwl example_inputs.yaml
```

### Usage

```bash
> toil-cwl-runner vardict_single_sample.cwl --help
usage: vardict_single_sample.cwl [-h] [--bedfile BEDFILE]
                                 [--input_bam_control INPUT_BAM_CONTROL]
                                 --input_bam_case INPUT_BAM_CASE
                                 --reference_fasta REFERENCE_FASTA
                                 [--sample_name SAMPLE_NAME]
                                 [--bed_file_column_for_region_start BED_FILE_COLUMN_FOR_REGION_START]
                                 [--bed_file_column_for_region_end BED_FILE_COLUMN_FOR_REGION_END]
                                 [--bed_file_column_for_gene_name BED_FILE_COLUMN_FOR_GENE_NAME]
                                 [--bed_file_column_for_chromsome BED_FILE_COLUMN_FOR_CHROMSOME]
                                 --control_sample_name CONTROL_SAMPLE_NAME
                                 [--filter_variants]
                                 [--minimum_allele_frequency MINIMUM_ALLELE_FREQUENCY]
                                 --output_vcf OUTPUT_VCF
                                 [job_order]

positional arguments:
  job_order             Job input json file

optional arguments:
  -h, --help            show this help message and exit
  --bedfile BEDFILE
  --input_bam_control INPUT_BAM_CONTROL
  --input_bam_case INPUT_BAM_CASE
  --reference_fasta REFERENCE_FASTA
  --sample_name SAMPLE_NAME
  --bed_file_column_for_region_start BED_FILE_COLUMN_FOR_REGION_START
  --bed_file_column_for_region_end BED_FILE_COLUMN_FOR_REGION_END
  --bed_file_column_for_gene_name BED_FILE_COLUMN_FOR_GENE_NAME
  --bed_file_column_for_chromsome BED_FILE_COLUMN_FOR_CHROMSOME
  --control_sample_name CONTROL_SAMPLE_NAME
  --filter_variants
  --minimum_allele_frequency MINIMUM_ALLELE_FREQUENCY
  --output_vcf OUTPUT_VCF
```


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