.. _`bio/bcftools/mpileup`:

BCFTOOLS MPILEUP
================


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

Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files.

**URL**: http://www.htslib.org/doc/bcftools.html#mpileup

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule bcftools_mpileup:
        input:
            alignments="mapped/{sample}.bam",
            ref="genome.fasta",  # this can be left out if --no-reference is in options
            index="genome.fasta.fai",
        output:
            pileup="pileups/{sample}.pileup.bcf",
        params:
            uncompressed_bcf=False,
            extra="--max-depth 100 --min-BQ 15",
        log:
            "logs/bcftools_mpileup/{sample}.log",
        wrapper:
            "v3.0.1/bio/bcftools/mpileup"

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 allows to specify that a BCF output should be uncompressed (ignored otherwise).
* The `extra` param allows for additional program arguments (not `--threads`, `-f/--fasta-ref`, `-o/--output`, or `-O/--output-type`).


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

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




Authors
-------

* Michael Hall
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Michael Hall"
    __copyright__ = "Copyright 2020, Michael Hall"
    __email__ = "michael@mbh.sh"
    __license__ = "MIT"


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


    extra = snakemake.params.get("extra", "")
    bcftools_opts = get_bcftools_opts(
        snakemake, parse_ref=("--no-reference" not in extra), parse_memory=False
    )
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)


    class MissingReferenceError(Exception):
        pass


    shell("bcftools mpileup {bcftools_opts} {extra} {snakemake.input[0]} {log}")


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