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. You can use phimtools as your own imputation pipeline in your local Linux cluster.

Quick start

phimtools use Eagle or beagle(requires Java version 8) for phasing and Minimac3 or Minimac4 for imputation.

Installation

Install the released version by pip:

pip install phimtools

This command will install phimtools in your system and you can use phimtools in your commandline.

Important notes before starting

Ensure that Eagle, beagle (requires Java version 8), and minimac4 (or minimac3) softwares are installed in your analysis environment.

• Eagle
  • download: https://alkesgroup.broadinstitute.org/Eagle/downloads/Eagle_v2.4.1.tar.gz
• beagle
  • Java executor: https://faculty.washington.edu/browning/beagle/beagle.28Jun21.220.jar
  • genetic_maps: http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/
• Minimac4
  • install: sudo apt install minimac4 or

  git clone https://github.com/statgen/Minimac4.git
  cd Minimac4
  bash install.sh
  

  • Reference Panels: https://genome.sph.umich.edu/wiki/Minimac4

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, 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 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 configuration file: 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.

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.

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.

phimtools impute -C config.yaml \
    -I your.vcf.gz \
    -O test_outprefix \
    --refpanel-version 1000G_P3_GRCh37 \
    --reference-build GRCh37 \
    --unprephase \
    --nCPU 4