Package: phimtools
phimtools: A phasing and imputation tools for NGS data.Introductionphimtoolsis a phasing and imputation tools for NGS data, which is the
main core of imputation server. You can use phimtools as your own imputation
pipeline in your local Linux cluster.Quick startphimtools useEagleorbeagle(requires Java version 8)
for phasing andMinimac3orMinimac4for imputation.InstallationInstall the released version by pip:pipinstallphimtoolsThis command will install phimtools in your system and you can usephimtoolsin your commandline.Important notes before startingEnsure that Eagle, beagle (requires Java version 8), and minimac4 (or minimac3) softwares are installed in your analysis environment.Eagledownload:https://alkesgroup.broadinstitute.org/Eagle/downloads/Eagle_v2.4.1.tar.gzbeagleJava executor:https://faculty.washington.edu/browning/beagle/beagle.28Jun21.220.jargenetic_maps:http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/Minimac4install:sudo apt install minimac4orgit clone https://github.com/statgen/Minimac4.git
cd Minimac4
bash install.shReference Panels:https://genome.sph.umich.edu/wiki/Minimac4UsageYou can find all the parameter for imputation process by runningphimtools 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, beagle]
  -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, GRCh38
  --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 filephimtoolsneeds 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 configuration file:config.yaml.Now you can usephimtoolsas your powerful imputation pipeline, once you
have finished the setting.ExamplesThis command would be enough for most of your jobs,--nCPUis for
setting the number of threads.phimtoolsimpute-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 runningphimtoolsin genome region:21:38347375-38500731and22:17203103-17439826.phimtoolsimpute-Cconfig.yaml\-Iyour.vcf.gz\-Otest_outprefix\--refpanel-version1000G_P3_GRCh37\--reference-buildGRCh37\--regions21:38347375-38500731,22:17203103-17439826\--nCPU4phimtoolswill 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--unprephaseargument to skip that process.phimtoolsimpute-Cconfig.yaml\-Iyour.vcf.gz\-Otest_outprefix\--refpanel-version1000G_P3_GRCh37\--reference-buildGRCh37\--unprephase\--nCPU4