.. _`bio/benchmark/chm-eval`:

CHM-EVAL
========


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

Evaluate given VCF file with chm-eval for benchmarking variant calling.

**URL**: https://github.com/lh3/CHM-eval

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule chm_eval:
        input:
            kit="resources/chm-eval-kit",
            vcf="{sample}.vcf",
        output:
            summary="chm-eval/{sample}.summary",  # summary statistics
            bed="chm-eval/{sample}.err.bed.gz",  # bed file with errors
        params:
            extra="",
            build="38",
        log:
            "logs/chm-eval/{sample}.log",
        wrapper:
            "v3.0.1/bio/benchmark/chm-eval"

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
---------------------

* ``perl=5.32.1``

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

* ``kit``: Path to annotation directory
* ``vcf``: Path to VCF to evaluate (can be gzipped)

**Output:**

* ``summary``: Path to statistics and evaluations
* ``bed``: Path to list of errors (BED formatted)



Params
------

* ``build``: Genome build. Either `37` or `38`.

* ``extra``: Optional parameters besides `-g`




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    __author__ = "Johannes Köster"
    __copyright__ = "Copyright 2020, Johannes Köster"
    __email__ = "johannes.koester@uni-due.de"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    kit = snakemake.input.kit
    vcf = snakemake.input.vcf
    build = snakemake.params.build
    extra = snakemake.params.get("extra", "")

    if not snakemake.output[0].endswith(".summary"):
        raise ValueError("Output file must end with .summary")
    out = snakemake.output[0][:-8]

    shell("({kit}/run-eval -g {build} -o {out} {extra} {vcf} | sh) {log}")


.. |nl| raw:: html

   <br>