The updates from WGSA v07 to v071 can be download from here. Steps for the updates are:
Step 1: Copy WGSA071.class to the WGSA folder, i.e. the folder where WGSA07.class locates.
Step 2: Copy all files under /WGSAdownload/WGSA071/resources/gnomAD/ to the resources/gnomAD folder, i.e. where the r2.0.1 files locate. You can delete all the r2.0.1 files if you will no longer run WGSA07.
Step 3: Copy all files under /WGSAdownload/WGSA071/resources/javaclass/ to the resources/javaclass folder.
To use the annovar version of spidex, please see this guidance.
Use WGSA071.class the same way as WGSA07: java WGSA071 [setting_file] <-m maximum_number_of_GB_memory_to_use> <-t maximum_number_of_threads_to_use> <-v hg19_or_hg38> <-i vcf_or_tsv>