Cleaning GWAS summary data

FOCUS relies on GWAS summary data having been 'prepared' for downstream TWAS+fine-mapping analyses. In order to do this we included a modified 'munge' tool from the LDSC software (FOCUS needs a few extra bells and whistles in its summary data compared with the original munge tool). At a minimum, FOCUS requires CHR, SNP, BP, A1 (effect allele), A2, BETA (or OR), and P to produce a munged GWAS data file.

In order to munge the data enter the command

focus munge GWAS.txt --output GWAS.cleaned

where GWAS.txt is the GWAS summary statistics data. This will create a munged, gzipped file GWAS.cleaned.sumstats.gz.

Please see the help command for more information and options for munging summary statistics data,

focus munge --help