Command Line Interface

HPG BigData allows you to process Fastq, BAM and VCF files, both in a local scenario and in a Hadoop cluster.

Assuming you are in the hpg-bigdata folder and for a Hadoop scenario, type the following command to see the available commands:

$ build/bin/hpg-bigdata.sh
Program:     HPG BigData for Hadoop (OpenCB)
Version:     0.2.0
Description: Hadoop-based tools for working with NGS data

Usage:       hpg-bigdata.sh [-h|--help] [--version] <command> <subcommand> [options]

Commands:
    sequence  Implements different tools for working with Fastq files
   alignment  Implements different tools for working with BAM files
     variant  Implements different tools for working with gVCF/VCF files

In a local scenario, you have to use the script:

$ build/bin/hpg-bigdata-local.sh