Introduction to SNP-based variant calling
==========================================

This pipeline contains a wrapper for `vivaxGEN NGS-Pipeline <https://github.com/vivaxgen/ngs-pipeline/>`_, a SNP-based variant
calling pipeline, which has been setup to process *P. vivax* sequence data.
This pipeline will produce ordinary VCF file that can be used for further
downstream analysis.

Currently, this pipeline was setup to use multi-step mode of vivaxGEN
NGS-Pipeline in a single command line with GATK-based workflow to generate VCF
file
There is also Freebayes-based workflow, but it requires modification of the
setting, which will not be covered in this documentation.

Quick Start
------------

#. Running the pipeline is as easy executing the following command:

.. code-block:: console

    $ ngs-pl run-discovery-variant-caller -o output_dir path_to_fastq/*.fastq.gz

#. When the command finishes, examine the content of ``output_dir`` directory:

The layout of the output directory is:

.. code-block:: console

    $ tree output_dir
    output_dir/
        metafile/
                manifest.tsv
        analysis/
                SAMPLE-1/
                    gvcf/
                        SAMPLE-1-PvP01_all_v2.g.vcf.gz
                        SAMPLE-1-PvP01_all_v2.g.vcf.gz.tbi
                    maps/
                        mapped-final.bam
                        mapped-final.bam.bai
                    reads/
                        raw-0_R1.fastq.gz
                        raw-0_R2.fastq.gz
                    logs/
                        ...
                SAMPLE-2/
                ...
        joint/
            concatenated.vcf.gz
            vcfs/
        reports/
            ...
        completed_samples/
            SAMPLE-1/
                ...
            SAMPLE-2/
                ...
        failed_samples/
            ...
        
The primary output file of interest is the ``concatenated.vcf.gz`` which contains the SNPs and the genotype calls for each of the samples.