SHAPEIT
4 years old with no update. No documenting. -Sean
SHAPEIT
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>
Running SHAPEIT in HPC
Interactive Job
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
...
Batch Job
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:
[1] SHAPEIT HOME
[2] SHAPEIT Tutorial