Package: pitools
Introductionpitoolsis 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 startpitools useeaglefor phasing
andMinimac3for imputation.InstallationInstall the released version by pip:pipinstallpitoolsOr you may instead want to install the development version from github,
by running:pipinstallgit+git://github.com/ShujiaHuang/pitools.git#egg=pitoolsThis command will install pitools in your system and you can usepitoolsin
your commandline.UsageYou can find all the parameter for imputation process by runningpitools 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 filepitoolsneeds 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.Now you can usepitoolsas your powerful imputation pipeline, once you
have finished the setting.ExamplesThis command would be enough for most of your jobs.pitoolsimpute-Cconfig.yaml\-Iyour.vcf.gz\-Otest_outprefix\--refpanel-version1000G_P3_GRCh37\--reference-buildGRCh37\--nCPU4What if you just want to preform the imputed process in some specific
regions. Here is an example for runningpitoolsin genome region:21:38347375-38500731and22:17203103-17439826.pitoolsimpute-Cconfig.yaml\-Iyour.vcf.gz\-Otest_outprefix\--refpanel-version1000G_P3_GRCh37\--reference-buildGRCh37\--regions21:38347375-38500731,22:17203103-17439826\--nCPU4PI 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--unprephaseargument to skip that process.pitoolsimpute-Cconfig.yaml\-Iyour.vcf.gz\-Otest_outprefix\--refpanel-version1000G_P3_GRCh37\--reference-buildGRCh37\--unprephase\--nCPU4