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"info": {
"author": "Shujia Huang",
"author_email": "huangshujia9@gmail.com",
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"classifiers": [
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Operating System :: POSIX",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 2.7",
"Programming Language :: Python :: 3.7",
"Topic :: Scientific/Engineering :: Bio-Informatics"
],
"description": "pitools: A phasing and imputation tools for NGS data.\n=====================================================\n\nIntroduction\n------------\n\n``pitools`` is a phasing and imputation tools for NGS data, which is the main\ncore of imputation server: https://imputation.cngb.org/. You can use pitools\nas your own imputation pipeline in your local Linux cluster.\n\nQuick start\n-----------\n\npitools use `eagle `__ for phasing \nand `Minimac3 `__ for imputation.\n\nInstallation\n~~~~~~~~~~~~\n\nInstall the released version by pip:\n\n.. code:: bash\n\n pip install pitools\n\nOr you may instead want to install the development version from github,\nby running:\n\n.. code:: bash\n\n pip install git+git://github.com/ShujiaHuang/pitools.git#egg=pitools\n\nThis command will install pitools in your system and you can use ``pitools`` in\nyour commandline.\n\nUsage\n~~~~~\n\nYou can find all the parameter for imputation process by running\n``pitools impute --help``:\n\n::\n\n usage: pitools impute [-h] -C CONFIG [-M IMPUTE_METHOD] [-P PHASE_METHOD] -I IN_VCF\n -O OUT_PREFIX --refpanel-version REFPANEL --reference-build\n REFBUILD [--unprephase] [--regions chr:start-end]\n [--nCPU NCPU]\n\n optional arguments:\n -h, --help show this help message and exit\n -C CONFIG, --conf CONFIG\n YAML configuration file specifying details information\n for imputation\n -M IMPUTE_METHOD, --methods IMPUTE_METHOD\n Tool for imputation. [minimac]\n -P PHASE_METHOD, --prephase-method PHASE_METHOD\n Tool for pre-phase before imputation. [eagle]\n -I IN_VCF, --input IN_VCF\n Input one VCF file to analyze. Required\n -O OUT_PREFIX, --outprefix OUT_PREFIX\n Prefix for output files. Required\n --refpanel-version REFPANEL\n The version of haplotype data for reference panel.\n Required\n --reference-build REFBUILD\n The build version of reference, e.g: GRCh37\n --unprephase Do not perform pre-phased before the imputation\n process.\n --regions chr:start-end\n Skip positions which not in these regions. This\n parameter could be a list of comma deleimited genome\n regions(e.g.: chr:start-end,chr:start-end)\n --nCPU NCPU Number of threads. [1]\n\nConfiguration file\n~~~~~~~~~~~~~~~~~~\n\n``pitools`` needs a configuration file for setting the path of phasing\nprogram, imputation program, reference version and reference panel.\nHere's one of the examples for how to create a config- uration file:\n`config.yaml <./tests/config.yaml>`__.\n\nNow you can use ``pitools`` as your powerful imputation pipeline, once you\nhave finished the setting.\n\nExamples\n~~~~~~~~\n\nThis command would be enough for most of your jobs.\n\n.. code:: bash\n\n pitools impute -C config.yaml \\\n -I your.vcf.gz \\\n -O test_outprefix \\\n --refpanel-version 1000G_P3_GRCh37 \\\n --reference-build GRCh37 \\\n --nCPU 4\n\nWhat if you just want to preform the imputed process in some specific\nregions. Here is an example for running ``pitools`` in genome region:\n``21:38347375-38500731`` and ``22:17203103-17439826``.\n\n.. code:: bash\n\n pitools impute -C config.yaml \\\n -I your.vcf.gz \\\n -O test_outprefix \\\n --refpanel-version 1000G_P3_GRCh37 \\\n --reference-build GRCh37 \\\n --regions 21:38347375-38500731,22:17203103-17439826 \\\n --nCPU 4\n\nPI will perform pre-phasing automatically before perform the imputation\nprocess. But sometimes your input VCF file has been phased already. And\nyou don't want to run it any more then you can set ``--unprephase``\nargument to skip that process.\n\n.. code:: bash\n\n pitools impute -C config.yaml \\\n -I your.vcf.gz \\\n -O test_outprefix \\\n --refpanel-version 1000G_P3_GRCh37 \\\n --reference-build GRCh37 \\\n --unprephase \\\n --nCPU 4\n\n",
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