SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

SHAPEIT has several notable features:

• Linear complexity with the number of SNPs and conditioning haplotypes.
• Whole chromosome GWAS scale datasets can be phased in a single run.
• Phasing individuals with any level of relatedness
• Phasing is multi-threaded to tailor computational times to your resources
• Handles X chromosomes phasing
• Phasing using a reference panel (eg.1,000 Genomes) to aid phasing
• Ideal for pre-phasing imputation together with IMPUTE2

References:

• SHAPEIT has primarily been developed by Dr Olivier Delaneau through a collaborative project between the research groups of Prof Jean-Francois Zagury at CNAM and Prof Jonathan Marchini at Oxford. Funding for this project has been received from several sources : CNAM,  Peptinov, MRC,  Leverhulme, The Wellcome Trust.

• https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html

• Module Name: shapeit (see the modules page for more information)
• Multithreaded
• Example files in /usr/local/apps/shapeit/example

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load shapeit
[user@cn3144 ~]$ shapeit --input-bed gwas.bed gwas.bim gwas.fam --input-map genetic_map.txt --output-max gwas.phased.haps gwas.phased.sample --thread $SLURM_CPUS_PER_TASK

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load shapeit
shapeit --input-bed gwas.bed gwas.bim gwas.fam --input-map genetic_map.txt --output-max gwas.phased.haps gwas.phased.sample --thread $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 [--mem=#] batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; shapeit --input-bed gwas.bed gwas.bim gwas.fam --input-map genetic_map.txt --output-max gwas.phased.haps gwas.phased.sample --thread $SLURM_CPUS_PER_TASK
cd dir2; shapeit --input-bed gwas.bed gwas.bim gwas.fam --input-map genetic_map.txt --output-max gwas.phased.haps gwas.phased.sample --thread $SLURM_CPUS_PER_TASK
cd dir3; shapeit --input-bed gwas.bed gwas.bim gwas.fam --input-map genetic_map.txt --output-max gwas.phased.haps gwas.phased.sample --thread $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f job.swarm [-g #] -t 4 --module shapeit