I am interested in using apex store to create covariate-adjusted LD matrices. To read the .vcov.bin files, it's my understanding that I will need to use Apex2R (#9). However, Apex2R assumes you have also performed the cis-eQTL mapping. I was hoping to combine these two analyses in a single step, but when I tried setting --make-vcov and/or --make-sumstats, it had no effect on the output files(checked with md5sum). Are these flags unimplemented?
$ bin/apex/apex store --help | head
bin/apex/apex {OPTIONS}
apex store: Store vcov (LD; variance-covariance) data.
OPTIONS:
-h, --help Display this help menu
Generating summary statistics
--make-vcov Generate variance-covariance files.
--make-sumstats Generate GWAS summary statistics.
I am interested in using
apex store
to create covariate-adjusted LD matrices. To read the.vcov.bin
files, it's my understanding that I will need to use Apex2R (#9). However, Apex2R assumes you have also performed the cis-eQTL mapping. I was hoping to combine these two analyses in a single step, but when I tried setting--make-vcov
and/or--make-sumstats
, it had no effect on the output files(checked withmd5sum
). Are these flags unimplemented?