Metadata-Version: 1.2
Name: pitools
Version: 1.0.0
Summary: pitools: A python program for phasing and imputation NGS data.
Home-page: https://github.com/ShujiaHuang/pitools
Author: Shujia Huang
Author-email: huangshujia9@gmail.com
Maintainer: Shujia Huang
Maintainer-email: huangshujia9@gmail.com
License: BSD (3-clause)
Download-URL: https://github.com/ShujiaHuang/pitools
Description: pitools: A phasing and imputation tools for NGS data.
        =====================================================
        
        Introduction
        ------------
        
        pitools is a phasing and imputation tools for NGS data, which is the main
        core of imputation server: https://imputation.cngb.org/. You can use pitools
        as your own imputation pipeline in your local Linux cluster.
        
        Quick start
        -----------
        
        pitools use `eagle <https://data.broadinstitute.org/alkesgroup/Eagle/>`__ for
        phasing and `Minimac3 <https://genome.sph.umich.edu/wiki/Minimac3>`__
        for imputation.
        
        Installation
        ~~~~~~~~~~~~
        
        Install the released version by pip:
        
        .. code:: bash
        
            pip install pitools
        
        Or you may instead want to install the development version from github,
        by running:
        
        .. code:: bash
        
            pip install git+git://github.com/ShujiaHuang/pitools.git#egg=pitools
        
        This command will install pitools in your system and you can use ``pitools`` in
        your commandline.
        
        Usage
        ~~~~~
        
        You can find all the parameter for imputation process by running
        ``pitools impute --help``:
        
        ::
        
            usage: pitools impute [-h] -C CONFIG [-M IMPUTE_METHOD] [-P PHASE_METHOD] -I IN_VCF
                             -O OUT_PREFIX --refpanel-version REFPANEL --reference-build
                             REFBUILD [--unprephase] [--regions chr:start-end]
                             [--nCPU NCPU]
        
            optional arguments:
              -h, --help            show this help message and exit
              -C CONFIG, --conf CONFIG
                                    YAML configuration file specifying details information
                                    for imputation
              -M IMPUTE_METHOD, --methods IMPUTE_METHOD
                                    Tool for imputation. [minimac]
              -P PHASE_METHOD, --prephase-method PHASE_METHOD
                                    Tool for pre-phase before imputation. [eagle]
              -I IN_VCF, --input IN_VCF
                                    Input one VCF file to analyze. Required
              -O OUT_PREFIX, --outprefix OUT_PREFIX
                                    Prefix for output files. Required
              --refpanel-version REFPANEL
                                    The version of haplotype data for reference panel.
                                    Required
              --reference-build REFBUILD
                                    The build version of reference, e.g: GRCh37
              --unprephase          Do not perform pre-phased before the imputation
                                    process.
              --regions chr:start-end
                                    Skip positions which not in these regions. This
                                    parameter could be a list of comma deleimited genome
                                    regions(e.g.: chr:start-end,chr:start-end)
              --nCPU NCPU           Number of threads. [1]
        
        Configuration file
        ~~~~~~~~~~~~~~~~~~
        
        ``pitools`` needs a configuration file for setting the path of phasing
        program, imputation program, reference version and reference panel.
        Here's one of the examples for how to create a config- uration file:
        `config.yaml <./tests/config.yaml>`__.
        
        Now you can use ``pitools`` as your powerful imputation pipeline, once you
        have finished the setting.
        
        Examples
        ~~~~~~~~
        
        This command would be enough for most of your jobs.
        
        .. code:: bash
        
            pitools impute -C config.yaml \
                -I your.vcf.gz \
                -O test_outprefix \
                --refpanel-version 1000G_P3_GRCh37 \
                --reference-build GRCh37 \
                --nCPU 4
        
        What if you just want to preform the imputed process in some specific
        regions. Here is an example for running ``pitools`` in genome region:
        ``21:38347375-38500731`` and ``22:17203103-17439826``.
        
        .. code:: bash
        
            pitools impute -C config.yaml \
                -I your.vcf.gz \
                -O test_outprefix \
                --refpanel-version 1000G_P3_GRCh37 \
                --reference-build GRCh37 \
                --regions  21:38347375-38500731,22:17203103-17439826 \
                --nCPU 4
        
        PI will perform pre-phasing automatically before perform the imputation
        process. But sometimes your input VCF file has been phased already. And
        you don't want to run it any more then you can set ``--unprephase``
        argument to skip that process.
        
        .. code:: bash
        
            pitools impute -C config.yaml \
                -I your.vcf.gz \
                -O test_outprefix \
                --refpanel-version 1000G_P3_GRCh37 \
                --reference-build GRCh37 \
                --unprephase \
                --nCPU 4
        
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.7
Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: POSIX
Classifier: Operating System :: POSIX :: Linux
