Which CNV_state to use from the output?

[aelhossiny]

Hi,

I noticed that joint_post and segs_consensus has multiple columns for the cnv_state, like (cnv_state, cnv_state_post, cnv_state_map, cnv_state_mle)

Which one is used for the final CNV event call?

Thanks

[teng-gao]

Hi,

The cnv_state reflects state assignment from HMM Viterbi decoding, whereas cnv_state_post reflects posterior state assignment after optimizing the extend of allelic imbalance ($\theta$) using Forward-Backward. cnv_state_post is always used as the final event type assignment. cnv_state in joint_post is copied from cnv_state_post from segs_consensus. The other columns are experimental and should not be used.

Best,
Teng