.. _`bio/freebayes`:

FREEBAYES
=========


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

Call small genomic variants with freebayes.

**URL**: https://github.com/freebayes/freebayes

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule freebayes:
        input:
            alns="mapped/{sample}.bam",
            idxs="mapped/{sample}.bam.bai",
            ref="genome.fasta",
        output:
            vcf = "calls/{sample}.vcf",
        log:
            "logs/freebayes/{sample}.log",
        params:
            normalize="-a",
        threads: 2
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/freebayes"


    rule freebayes_bcf:
        input:
            alns="mapped/{sample}.bam",
            ref="genome.fasta",
        output:
            bcf="calls/{sample}.bcf",
        log:
            "logs/freebayes/{sample}.bcf.log",
        threads: 2
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/freebayes"


    rule freebayes_bed:
        input:
            alns="mapped/{sample}.bam",
            ref="genome.fasta",
            regions="regions.bed",
        output:
            vcf="calls/{sample}.vcf.gz",
        log:
            "logs/freebayes/{sample}.bed.log",
        params:
            chunksize=50000,
        threads: 2
        resources:
            mem_mb=1024,
        wrapper:
            "v3.0.1/bio/freebayes"

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

* ``freebayes=1.3.6``
* ``bcftools=1.15``
* ``vcflib=1.0.3``
* ``htslib=1.16``
* ``parallel=20230722``
* ``bedtools=2.31.0``
* ``sed=4.8``
* ``snakemake-wrapper-utils=0.6.2``

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

* SAM/BAM/CRAM file(s)
* reference genome

**Output:**

* VCF/VCF.gz/BCF file



Params
------

* ``extra``: additional arguments for freebayes

* ``normalize``: use `bcftools norm` to normalize indels (one of `-a`, `-f`, `-m`, `-D` or `-d` must be used)

* ``chunkzise``: reference genome chunk size for parallelization (default `100000`)




Authors
-------

* Johannes Köster
* Felix Mölder
* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Johannes Köster, Felix Mölder, Christopher Schröder"
    __copyright__ = "Copyright 2017, Johannes Köster"
    __email__ = "johannes.koester@protonmail.com, felix.moelder@uni-due.de"
    __license__ = "MIT"


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


    log = snakemake.log_fmt_shell(stdout=False, stderr=True)
    extra = snakemake.params.get("extra", "")
    bcftools_sort_opts = get_bcftools_opts(
        snakemake,
        parse_threads=False,
        parse_ref=False,
        parse_regions=False,
        parse_samples=False,
        parse_targets=False,
        parse_output=False,
        parse_output_format=False,
    )


    pipe = ""
    norm_params = snakemake.params.get("normalize")
    if norm_params:
        bcftools_norm_opts = get_bcftools_opts(
            snakemake, parse_regions=False, parse_targets=False, parse_memory=False
        )
        pipe = f"bcftools norm {bcftools_norm_opts} {norm_params}"
    else:
        bcftools_view_opts = get_bcftools_opts(
            snakemake,
            parse_ref=False,
            parse_regions=False,
            parse_targets=False,
            parse_memory=False,
        )
        pipe = f"bcftools view {bcftools_view_opts}"


    if snakemake.threads == 1:
        freebayes = "freebayes"
    else:
        chunksize = snakemake.params.get("chunksize", 100000)
        regions = f"<(fasta_generate_regions.py {snakemake.input.ref}.fai {chunksize})"

        if snakemake.input.get("regions"):
            regions = (
                "<(bedtools intersect -a "
                + r"<(sed 's/:\([0-9]*\)-\([0-9]*\)$/\t\1\t\2/' "
                + f"{regions}) -b {snakemake.input.regions} | "
                + r"sed 's/\t\([0-9]*\)\t\([0-9]*\)$/:\1-\2/')"
            )

        freebayes = f"freebayes-parallel {regions} {snakemake.threads}"


    with TemporaryDirectory() as tempdir:
        shell(
            "({freebayes}"
            " --fasta-reference {snakemake.input.ref}"
            " {extra}"
            " {snakemake.input.alns}"
            " | bcftools sort {bcftools_sort_opts} --temp-dir {tempdir}"
            " | {pipe}"
            ") {log}"
        )


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