.. _`variant-calling-ampliseq (✓ production)`:

VARIANT-CALLING-AMPLISEQ (✓ PRODUCTION)
=======================================

Version: 1.0.0
Tags: AmpliSeq / Variant Calling / Flamingo / Automated

This is the fully automated pipeline for Ampliseq on Flamingo.
No config, no design, no time wasted.

« A good pipeline has no documentation » Someone at BiGR


.. 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 ==3.9.2
  
  * conda-forge::git ==2.30.2
  
  * conda-forge::jinja2 ==2.11.3
  
  * conda-forge::pygraphviz ==1.7
  
  * conda-forge::flask ==1.1.2
  
  * conda-forge::pandas ==1.2.3
  
  * conda-forge::zlib ==1.2.11
  
  * conda-forge::openssl ==1.1.1k
  
  * conda-forge::networkx ==2.5.1
  
  * bioconda::snakemake ==6.1.1
  
  * conda-forge::black ==20.8b1
  
  * conda-forge::singularity ==3.7.1
  
  * conda-forge::mamba ==0.9.2
  


Additionally, the following prerequisites are non-optional:


* None. Everything is on Flamingo already.




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

Please find below the list of required input files:


* Several **paried** fastq files.



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

Please find below the list of expected output files:


* Annotated VCF files

* MultiQC report




Notes
-----

This pipeline takes the cold storage into account. No need to copy your data in advance.

No maftools compatibility at this point.

List of tools:
rsync/ln -> Fastp -> BWA -> Samtools/GATK/Picard -> Mutect2/Vascan2 -> Snpsift/SnpEff -> MultiQC

Bam files are corrected before Varscan2 with GATK pipeline.
Raw bam are passed to Mutect2 since GATK advises to do so.

Mutect2 calling are filtered following best practices. Varscan2 calling are
filtered on padj <= 0.05.





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
  * - none
    - .. code-block:: bash 

        # No installation needed.



Testing
-------

In order to test the pipeline, you may try the following commands:

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

  * - Case
    - Command line
  * - quick-test
    - .. code-block:: bash 

        bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/variant_calling_ampliseq/test.sh
  * - verbose-test
    - .. code-block:: bash 

        bash -x /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/variant_calling_ampliseq/test.sh




Preparation
-----------

In order to prepare a run, you may try the following commands:

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

  * - Case
    - Command line
  * - none
    - .. code-block:: bash 

        # No preparation, everything is available.



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)
  * - hg19
    - .. code-block:: bash 

        bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/variant_calling_ampliseq/run.sh hg19
  * - hg38
    - .. code-block:: bash 

        bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/variant_calling_ampliseq/run.sh hg38