.. _`bio/vardict`:

VARDICT
=======


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/vardict?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/vardict

Run Vardict to call genomic variants


Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule vardict_single_mode:
        input:
            reference="data/genome.fasta",
            regions="regions.bed",
            bam="mapped/{sample}.bam",
        output:
            vcf="vcf/{sample}.s.vcf",
        params:
            extra="",
            bed_columns="-c 1 -S 2 -E 3 -g 4",  # Optional, default is -c 1 -S 2 -E 3 -g 4
            allele_frequency_threshold="0.01",  # Optional, default is 0.01
        threads: 1
        log:
            "logs/varscan_{sample}_s_.log",
        wrapper:
            "v3.0.1/bio/vardict"


    rule vardict_paired_mode:
        input:
            reference="data/genome.fasta",
            regions="regions.bed",
            bam="mapped/{sample}.bam",
            normal="mapped/b.bam",
        output:
            vcf="vcf/{sample}.tn.vcf",
        params:
            extra="",
        threads: 1
        log:
            "logs/varscan_{sample}_tn.log",
        wrapper:
            "v3.0.1/bio/vardict"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``vardict-java=1.8.3``

Input/Output
------------
**Input:**

* reference file
* bam file
* normal file, optional (must be set for tumor/normal mode)
* region file

**Output:**

* A VCF file



Params
------

* ``extra. optional``: 

* ``bed_columns, optional, default -c 1 -S 2 -E 3 -g 4``: 

* ``ah_th optional, default values is 0.01``: 




Authors
-------

* Patrik Smeds


Code
----

.. code-block:: python

    """Snakemake wrapper for VarDict Single sample mode"""

    __author__ = "Patrik Smeds"
    __copyright__ = "Copyright 2021, Patrik Smeds"
    __email__ = "patrik.smeds@scilifelab.uu.se"
    __license__ = "MIT"

    from pathlib import Path
    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=False, stderr=True)

    reference = snakemake.input.reference
    regions = snakemake.input.regions
    bam = snakemake.input.bam
    normal = snakemake.input.get("normal", None)
    vcf = snakemake.output.vcf

    extra = snakemake.params.get("extra", "")
    bed_columns = snakemake.params.get("bed_columns", "-c 1 -S 2 -E 3 -g 4")
    af_th = snakemake.params.get("allele_frequency_threshold", "0.01")


    if normal is None:
        input_bams = bam
        name = snakemake.params.get("sample_name", Path(bam).stem)
        post_scripts = (
            "teststrandbias.R | var2vcf_valid.pl -A -N '" + name + "' -E -f " + af_th
        )
    else:
        input_bams = "'" + bam + "|" + normal + "'"
        name = snakemake.params.get("sample_name", Path(bam).stem + "|" + Path(normal).stem)
        post_scripts = 'testsomatic.R | var2vcf_paired.pl -N "' + name + '" -f ' + af_th


    shell(
        "vardict-java -G {reference} "
        "-f {af_th} "
        " {extra} "
        "-th {snakemake.threads} "
        "{bed_columns} "
        "-N '{name}' "
        "-b {input_bams} "
        "{regions} |"
        "{post_scripts} "
        "> {vcf}"
        "{log}"
    )


.. |nl| raw:: html

   <br>