.. _`bio/whatshap/haplotag`:

WHATSHAP HAPLOTAG
=================


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

Phase BAM records by haplotype. For more information about whatshap see `whatshap documentation <https://whatshap.readthedocs.io/en/latest/guide.html#whatshap-haplotag>`_.

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

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule whatshap_haplotag:
        input:
            "phased.vcf.gz.tbi",
            "alignment.bam.bai",
            "reference.fasta.fai",
            vcf ="phased.vcf.gz",
            aln ="alignment.bam",
            ref = "reference.fasta"
        output:
            "alignment.phased.bam"
        params:
            extra="" # optionally use --ignore-linked-read, --tag-supplementary, etc.
        log:
            "logs/haplotag.10X.phased.log"
        threads: 4
        wrapper:
            "v3.0.1/bio/whatshap/haplotag"

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

* ``whatshap=2.1``

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

* ``vcf``: Path to vcf.gz/bcf file of phased SNPs.
* Path to vcf index file (.tbi for vcf.gz, .csi for .bcf).
* ``aln``: Path to alignments for the sample in BAM/CRAM format.
* Path to alignment index file in .bai/.crai format.
* ``ref``: Path to FASTA reference used to create vcf file.
* Path to FASTA index file in .fai format

**Output:**

* P
* a
* t
* h
*  
* t
* o
*  
* o
* u
* t
* p
* u
* t
*  
* p
* h
* a
* s
* e
* d
*  
* B
* A
* M
*  
* f
* i
* l
* e
* .



Params
------

* ``extra``: additional program arguments (e.g. `--ignore-linked-read` to ignore BX tag, `--linked-read-distance-cutoff` to set distance after which to split molecules with same BX tag, `--ignore-read-groups`, `--sample SAMPLE` to only phase this sample, `--tag-supplementary` to also tag supplementary alignments.




Authors
-------

* Pavel Dimens


Code
----

.. code-block:: python

    """Snakemake wrapper for whatshap haplotag."""

    __author__ = "Pavel Dimens"
    __copyright__ = "Copyright 2023, Pavel Dimens"
    __email__ = "pdimens@gmail.com"
    __license__ = "MIT"

    from snakemake.shell import shell

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

    shell(
        "whatshap haplotag"
        "{extra} "
        "--output-threads={snakemake.threads} "
        "-o {snakemake.output} "
        "--reference {snakemake.input.ref} "
        "{snakemake.input.vcf} "
        "{snakemake.input.aln} "
        "{log}"
    )


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