.. _`bio/deepvariant`:

DEEPVARIANT
===========

.. image:: https://img.shields.io/badge/blacklisted-make_examples.py%20does%20not%20find%20numpy-red

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

Call genetic variants using deep neural network. Copyright 2017 Google LLC. BSD 3-Clause "New" or "Revised" https://github.com/google/deepvariant



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule deepvariant:
        input:
            bam="mapped/{sample}.bam",
            ref="genome/genome.fasta"
        output:
            vcf="calls/{sample}.vcf.gz"
        params:
            model="wgs",   # {wgs, wes, pacbio, hybrid}
            sample_name=lambda w: w.sample, # optional
            extra=""
        threads: 2
        log:
            "logs/deepvariant/{sample}/stdout.log"
        wrapper:
            "v3.0.1/bio/deepvariant"


    rule deepvariant_gvcf:
        input:
            bam="mapped/{sample}.bam",
            ref="genome/genome.fasta"
        output:
            vcf="gvcf_calls/{sample}.vcf.gz",
            gvcf="gvcf_calls/{sample}.g.vcf.gz"
        params:
            model="wgs",   # {wgs, wes, pacbio, hybrid}
            extra=""
        threads: 2
        log:
            "logs/deepvariant/{sample}/stdout.log"
        wrapper:
            "v3.0.1/bio/deepvariant"

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.


Notes
-----

* The `extra` param alllows for additional program arguments.
* This snakemake wrapper uses bioconda deepvariant package. Copyright 2018 Brad Chapman.


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

* ``deepvariant=1.4``
* ``numpy=1.23``

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

* fasta
* bam

**Output:**

* vcf
* visual report html




Authors
-------

* Tetsuro Hisayoshi
* Nikos Tsardakas Renhuldt


Code
----

.. code-block:: python

    __author__ = "Tetsuro Hisayoshi"
    __copyright__ = "Copyright 2020, Tetsuro Hisayoshi"
    __email__ = "hisayoshi0530@gmail.com"
    __license__ = "MIT"

    import os
    import tempfile
    from snakemake.shell import shell

    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    extra = snakemake.params.get("extra", "")

    log_dir = os.path.dirname(snakemake.log[0])
    output_dir = os.path.dirname(snakemake.output[0])

    # sample name defaults to basename
    sample_name = snakemake.params.get(
        "sample_name", os.path.splitext(os.path.basename(snakemake.input.bam))[0]
    )


    make_examples_gvcf = postprocess_gvcf = ""
    gvcf = snakemake.output.get("gvcf", None)
    if gvcf:
        make_examples_gvcf = "--gvcf {tmp_dir} "
        postprocess_gvcf = (
            "--gvcf_infile {tmp_dir}/{sample_name}.gvcf.tfrecord@{snakemake.threads}.gz "
            "--gvcf_outfile {snakemake.output.gvcf} "
        )

    with tempfile.TemporaryDirectory() as tmp_dir:
        shell(
            "(dv_make_examples.py "
            "--cores {snakemake.threads} "
            "--ref {snakemake.input.ref} "
            "--reads {snakemake.input.bam} "
            "--sample {sample_name} "
            "--examples {tmp_dir} "
            "--logdir {log_dir} " + make_examples_gvcf + "{extra} \n"
            "dv_call_variants.py "
            "--cores {snakemake.threads} "
            "--outfile {tmp_dir}/{sample_name}.tmp "
            "--sample {sample_name} "
            "--examples {tmp_dir} "
            "--model {snakemake.params.model} \n"
            "dv_postprocess_variants.py "
            "--ref {snakemake.input.ref} "
            + postprocess_gvcf
            + "--infile {tmp_dir}/{sample_name}.tmp "
            "--outfile {snakemake.output.vcf} ) {log}"
        )


.. |nl| raw:: html

   <br>