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LDSC
Overview
LDSC is a python package for estimating heritability and genetic correlation from GWAS summary statistics. LDSC also computes LD Scores.
The master branch for version 1.0.0 (commit cf1707e from 02-May-17) is installed on the CSF.
Restrictions on use
There are no restrictions on access the software on the CSF. It is release under the GNU GPL v3 license so all use should adhere to that license.
Set up procedure
To access the software you must first load one of the modulefiles given below. Note that LDSC must be run with Anaconda python 2.5.0 and above. Hence one of the modulefiles below will automatically load the anaconda modulefile and one will require that you load your preferred version of anaconda before loading the LDSC modulefile.
# Will automatically load the Anaconda 2.5.0 (python 2.7.11) modulefile for you module load apps/gcc/python-packages/anaconda-2.5.0/ldsc/1.0.0-170502 # Requires that you have already loaded an Anaconda modulefile before loading this one module load apps/gcc/python-packages/anaconda-2.5.0/ldsc/1.0.0-170502-any-conda
See below for how to run the ldsc.py script.
The modulefiles will also set an environment variable named $LDSCDIR allowing easy access to the ContinuousAnnotations scripts in the installation:
ls $LDSCDIR/ContinuousAnnotations/ # Other scripts and files are available in the installation via: ls $LDSCDIR
To see the command-line flags / args that the scripts require you may run the following on the login node (but no data processing should be done there):
ldsc.py -h munge_sumstats.py -h
Running the application
Please do not run LDSC on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings # The LDSC main script ldsc.py arg1 arg2 ... # Or the stats script: munge_sumstats.py arg1 arg2 ...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.