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Welcome to the focus wiki!

Here you'll find details on how to import weights, train weights using your own data, clean summary GWAS, and perform fine-mapping on TWAS results.

Please see the sidebar for links to each.

We recommend using reference LD from LDSC. From the command line this can be done as

wget https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_plinkfiles.tgz
tar -xvzf 1000G_Phase3_plinkfiles.tgz

We recommend using a multiple tissue, multiple eQTL reference panel weight database here. This combines GTExv7 weights from PrediXcan with METSIM, NTR, YFS, and CMC weights from FUSION software into a single usable database for FOCUS.

wget https://www.dropbox.com/s/ep3dzlqnp7p8e5j/focus.db?dl=0
mv focus.db?dl=0 focus.db