Welcome to the
GenomicSEM is software to estimate a structural equation model on traits, for which you only have access to GWAS summary statistics.
There are two primary types of models in
GenomicSEM: one that includes the effect of individual SNPs and one that does not include SNP effects. Please see the tutorials for Models with SNP Effects and Models without SNP effects for details on how to run each. Answers to common questions can be found on the FAQs page (which we will launch as soon as we frequently get actual questions). If you are having issues and not finding the answers anywhere on the wiki or FAQs page, we encourage you to post your question on the google group.
Code Update: On March 10th, 2019 we corrected a bug which impacts the weights used in ld-score regression and caused estimates produced to vary slightly. Substantive results are unlikely to be impacted, but we recommend reinstalling Genomic SEM if it was installed prior to this date.
Contents of the wiki:
Learn how to install
Consider some of the nuances of summary data, and know where to find summary data.
Fit SEM models to GWAS summary data without a SNP
Run a GWAS where the SNP is included in the structural equation model.
Run a GWAS with the SNP effect(s) included in a user specified SEM
Get guidance on advanced models on this page with tutorials which showcases and explains specific structural equation models you can fit using
PGC worldwide lab meeting on genomicSEM
Click below for a video which provides an introduction to the method/paper: