SHAPEIT

4 years old with no update. No documenting. -Sean

SHAPEIT [1] is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

Installed Versions

All the available versions of SHAPEIT for use can be viewed by issuing the following command. This applies for other applications as well.

module avail shapeit

output:

---------------------- /usr/local/share/modulefiles -------------------------

shapeit/v2.r79

The default version is identified by "(default)" behind the module name and can be loaded as:

module load shapeit

The other versions of SHAPEIT can be loaded as:

module load shapeit/<version>

Request a node

qsub -I

load the module

module load shapeit

See the command options

shapeit --help

output:

Segmented HAPlotype Estimation & Imputation Tool

* Authors : Olivier Delaneau, Jared O'Connell, Jean-François Zagury, Jonathan Marchini

* Contact : send an email to the OXSTATGEN mail list https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=OXSTATGEN

* Webpage : https://mathgen.stats.ox.ac.uk/shapeit

* Version : v2.r790

Basic options:

-H [ --help ] Produce help message.

--licence Produce licence description.

--version Produce version number.

--source Produce source file version details.

--seed arg (=1453239577) Seed of the random number gene

...

Copy the directory "SHAPEIT" from /usr/local/doc and cd to it

cp -r /usr/local/doc/SHAPEIT .

cd SHAPEIT

Untar the tutorial package [2]

tar zxvf SHAPEIT+IMPUTE.pre-phasing.examples.tgz

Run the job

qsub job.pbs

You will get the output log file slurm-<jobid>.out with output files.

References: