Metadata-Version: 2.1
Name: phimtools
Version: 1.0.2
Summary: phimtools: A python program for phasing and imputation NGS data.
Home-page: https://github.com/ShujiaHuang/phimtools
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/phimtools
Description: phimtools: A phasing and imputation tools for NGS data.
        =====================================================
        
        Introduction
        ------------
        
        `phimtools` is a phasing and imputation tools for NGS data, which is the
        main core of imputation server: <https://imputation.cngb.org/>. You can
        use phimtools as your own imputation pipeline in your local Linux cluster.
        
        Quick start
        -----------
        
        phimtools 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:
        
        ```bash
        pip install phimtools
        ```
        
        Or you may instead want to install the development version from github,
        by running:
        
        ```bash
        pip install git+git://github.com/ShujiaHuang/phimtools.git#egg=phimtools
        ```
        
        This command will install phimtools in your system and you can use
        `phimtools` in your commandline.
        
        ### Usage
        
        You can find all the parameter for imputation process by running
        `phimtools impute --help`:
        
            usage: phimtools 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
        
        `phimtools` 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 `phimtools` as your powerful imputation pipeline, once you
        have finished the setting.
        
        ### Examples
        
        This command would be enough for most of your jobs, `--nCPU` is for
        setting the number of threads.
        
        ```bash
        phimtools 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 `phimtools` in genome region:
        `21:38347375-38500731` and `22:17203103-17439826`.
        
        ```bash
        phimtools 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
        ```
        
        `phimtools` 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 again then you can set
        `--unprephase` argument to skip that process.
        
        ```bash
        phimtools 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
Description-Content-Type: text/markdown
