.. _`dna-seq-gatk-variant-calling (⚠ Foreign importation)`:

DNA-SEQ-GATK-VARIANT-CALLING (⚠ FOREIGN IMPORTATION)
====================================================

Version: 1.0.1
Tags: DNA-Seq / Variant Calling / GATK

This Snakemake pipeline implements the [GATK best-practices workflow](https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145) for calling small genomic variants.

You may find more information at:
  * Github: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145


.. role:: bash(code)
  :language: bash

Pipeline dependencies
---------------------

This pipeline requires the following packages to be run. Any other additional requirements are being installed dynamically.

Conda:
  
  * conda-forge::python=3.7.3
  
  * conda-forge::pytest=5.1.2
  
  * conda-forge::datrie=0.8
  
  * conda-forge::git=2.20.1
  
  * conda-forge::jinja2=2.10.1
  
  * conda-forge::pygraphviz=1.5
  
  * conda-forge::flask=1.1.1
  
  * conda-forge::pandas=0.25.1
  
  * conda-forge::zlib=1.2.11
  
  * conda-forge::openssl=1.1.1c
  
  * conda-forge::networkx=2.3
  
  * bioconda::snakemake=5.5.4
  


Additionally, the following prerequisites are non-optional:


* Conda

* Genome sequence

* Known variant sites




Input files
-----------

Please find below the list of required input files:


* Fastq formatted reads (one or multiple ones)

* A fasta formatted genome sequence, its index and dictionnary.

* A VCF formatted known variant file



Output files
------------

Please find below the list of expected output files:


* Multiple html reports

* VCF files

* BAM files




Notes
-----

This pipeline comes from the Snakemake workflows: https://github.com/snakemake-workflows/docs





Installation
------------

While installing the workflow, you may run the following commands (order matters):

.. list-table::
  :widths: 10 80
  :header-rows: 1
  :align: left

  * - Case
    - Command line
  * - git
    - .. code-block:: bash 

        # This command clones the git repository

        if [ ! -d "${DNA_SEQ_GATK_VARIANT_CALLING:?}" ]; then git clone https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling.git "${DNA_SEQ_GATK_VARIANT_CALLING:?}"; fi
  * - conda
    - .. code-block:: bash 

        # This command create conda virtual environment,

        # but requires available git repository (see above)

        conda env create --force --file "${STRONGR_DIR:?}/workflows/calling/dna-seq-gatk-variant-calling/environment.yaml






Execution
---------

In order to execute the pipeline, you may run the following commands:

.. list-table::
  :widths: 10 80
  :header-rows: 1
  :align: left

  * - Case
    - Command line(s)
  * - local
    - .. code-block:: bash 

        snakemake --use-conda -pr