.. _`bio/delly`:

DELLY
=====


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

Call variants with delly.

**URL**: https://github.com/dellytools/delly

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule delly_bcf:
        input:
            ref="genome.fasta",
            alns=["mapped/a.bam"],
            # optional
            exclude="human.hg19.excl.tsv",
        output:
            "sv/calls.bcf",
        params:
            uncompressed_bcf=True,
            extra="",  # optional parameters for delly (except -g, -x)
        log:
            "logs/delly.log",
        threads: 2  # It is best to use as many threads as samples
        wrapper:
            "v3.0.1/bio/delly"


    rule delly_vcfgz:
        input:
            ref="genome.fasta",
            alns=["mapped/a.bam"],
            # optional
            exclude="human.hg19.excl.tsv",
        output:
            "sv/calls.vcf.gz",
        params:
            extra="",  # optional parameters for delly (except -g, -x)
        log:
            "logs/delly.log",
        threads: 2  # It is best to use as many threads as samples
        wrapper:
            "v3.0.1/bio/delly"

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 `uncompressed_bcf` param sets output to uncompressed BCF (ignored if output is `vcf` or `vcf.gz`)
* The `extra` param allows for additional program arguments


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

* ``delly=1.1.8``
* ``bcftools=1.18``
* ``snakemake-wrapper-utils=0.6.2``

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

* BAM/CRAM file(s)
* reference genome
* BED file (optional)

**Output:**

* VCF/BCF with SVs.




Authors
-------

* Johannes Köster
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2016, Johannes Köster"
    __email__ = "koester@jimmy.harvard.edu"
    __license__ = "MIT"


    from snakemake.shell import shell
    from snakemake_wrapper_utils.bcftools import get_bcftools_opts


    bcftools_opts = get_bcftools_opts(snakemake, parse_ref=False, parse_memory=False)
    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)


    exclude = snakemake.input.get("exclude", "")
    if exclude:
        exclude = f"-x {exclude}"


    shell(
        "(OMP_NUM_THREADS={snakemake.threads} delly call"
        " -g {snakemake.input.ref}"
        " {exclude}"
        " {extra}"
        " {snakemake.input.alns} | "
        # Convert output to specified format
        "bcftools view"
        " {bcftools_opts}"
        ") {log}"
    )


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