### Download the repository

Source: https://github.com/chrismaherlab/pact/blob/master/README.md

Command to download the PACT repository.

```bash
git clone https://github.com/ChrisMaherLab/PACT.git
```

--------------------------------

### Samtools faidx command

Source: https://github.com/chrismaherlab/pact/blob/master/README.md

Command to create a reference genome index file.

```bash
samtools faidx
```

--------------------------------

### SnpEff download command

Source: https://github.com/chrismaherlab/pact/blob/master/README.md

Command to download snpEff annotation databases.

```bash
java -jar snpEff.jar download <database>
```

--------------------------------

### Tabix command

Source: https://github.com/chrismaherlab/pact/blob/master/README.md

Command to create a tabix index for a VCF file.

```bash
tabix -p
```

--------------------------------

### Run CWL pipelines with Cromwell

Source: https://github.com/chrismaherlab/pact/blob/master/README.md

Command to run CWL pipelines using the Cromwell interpreter.

```bash
java -Dconfig.file=<config.file> -jar <cromwell.jar> run -t cwl -i <input_yaml> pipelines/<pipeline>.cwl
```

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