PHASE reconstructs haplotypes from population genotype data using a Bayesian statistical model that considers the decay of LD with distance due to recombination. Inputs can include biallelic SNPs as well as multi-allelic loci like SNPs with more than two alleles, HLA allels, or microsatellites.

References:

• M. Stephens, M. Smith, and P. Donnelly. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics 2001, 68:978-989. Pubmed |  PMC |  Journal
• M. Stephens, P. Scheet. Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation. American Journal of Human Genetics 2005, 76:449-462. Pubmed |  PMC |  Journal

• Manual

• Module Name: phase (see the modules page for more information)
• Example files in $PHASE_TEST_DATA

Allocate an interactive session, load the phase module and analyze a simple test data set running 1000 iterations

[user@biowulf]$ sinteractive --gres=lscratch:5
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@cn3114]$ module load phase/2.1.1
[user@cn3114]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3114]$ cp $PHASE_TEST_DATA/test.inp .
[user@cn3114]$ PHASE test.inp test.out 1000
Reading in data
Reading Positions of loci
Reading individual      3
Finished reading
Computing matrix Q, please wait
Done computing Q
3
5
MSSSM
0 #1
12 0 0 1 3
11 1 1 0 3
0 #2
12 0 1 1 3
12 1 0 0 2
0 #3
12 1 0 1 2
12 0 1 0 13
Resolving with method R
Making List of all possible haplotypes
Method = R
Performing Final Set of Iterations... nearly there!
Performing Burn-in iterations
  50% done
Estimating recom rates
Continuing Burn-in
Performing Main iterations
Writing output to files
Producing Summary, please wait

[user@cn3114]$ ls -1 test.out*
test.out
test.out_freqs
test.out_hbg
test.out_monitor
test.out_pairs
test.out_probs
test.out_recom

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

The input format and options are described in the manual.

Create a batch input file (e.g. phase.sh), which uses the input file 'phase.in'. For example:

#! /bin/bash

module load phase/2.1.1 || exit 1
PHASE input output 1000

Submit this job using the Slurm sbatch command.

sbatch phase.sh

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

PHASE -X10 input1 output1
PHASE -X10 input2 output2

Submit this job using the swarm command.

swarm -f phase.swarm -g 4 -t 1 -p 2 --module phase/2.1.1