Status of `--make-vcov` and `--make-sumstats` flags to `apex store`

[jdblischak]

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.