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LDpred

Description

LDpred is a Python based software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium (LD).

Source

How to Use

There are multiple versions of LDpred available. An easy way of selecting the version is to use environment modules. To see the versions available, type

module avail LDpred

To select a version, type

module load LDpred/[ver]

where [ver] is the version of choice.

Commands

Example

Simulated test data can be found in the $LDPRED_HOME/test_data directory.

$ module load LDpred
$ cp $LDPRED_HOME/test_data/* .
$ coord_genotypes.py --gf=LDpred_data_p0.001_test_0 --ssf=LDpred_data_p0.001_ss_0.txt --N=100 --out=bogus.hdf5

Documentation