Step 2. Calculate superpopulation frequencies using tgp_calculate_within_frqs.wdl
- note that this will remove all duplicated ids, see: Why are there duplicate calls in the phase 3 call set? | 1000 Genomes, as otherwise duplicated ids will mess with SCOPE estimation supervised
This is a companion discussion topic for the original entry at github.com/blostein/tgp_calculate_freq/tgp_calculate_within_frqs