CERC-Genomic-Medicine / shapeit4_pipeline

Pipeline for genotype phasing using SHAPEIT4

Genotype phasing pipeline

1. Description

Pipeline for genotype phasing using SHAPEIT4. The pipeline automatically chunks chromosomes into overlapping regions, distributes chunks for phasing accross multiple compute nodes, and concatinates chunks based on overlapping flanking regions. The pipeline was developed using Nextflow and was tested on SLURM job scheduler.

2. Prerequisites

The following software is required:

• Nextflow
• bcftools

3. Installation

To run this pipline you will need:

1. Download and install (SHAPEIT4](https://odelaneau.github.io/shapeit4/)

4. Execution

1. Modify nextflow.config configuration file:

• params.unphased_vcfs -- path to VCF/BCF files with unphased genotypes. Each VCF/BCF file must have the corresponding tbi/csi index.
• params.window -- size of the chromosome chunk in base-pairs for distributed phasing. See SHAPEIT4 documentation for details.
• params.flank -- size of the flanking region around chunk in base-pairs.
• params.shapeit_exec -- path to the SHAPEIT4 executable
• params.shapeit_maps -- path to the SHAPEIT4 folder with genetic maps. NOTE: For GRCh37, you need to modify shapeit command line inside phase_chunks process in Phasing.nf.
• process.* and executor.* -- set this arguments according to your compute cluster configuration.

2. Run pipleine. Example of interactive SLURM job:

salloc --time=12:00:00 --ntasks=1 --mem-per-cpu=16G
module load nextflow
module load bcftools
nextflow run Phasing.nf