Allele specific copy numbers for 'amp' and calculation of cnv_state_post

[kzb193]

Hello Dr. Gao,

Can you please help me out with the following queries regarding the outputs from Numbat?

1. How can I extract the estimated allele specific copy numbers for 'amp'? For example, I am interested in the allele specific copy number [ (1,2) or (1,3) ] for 'cnv_state_post'='amp' in segs_consensus_2.tsv or 'cnv_state'='amp' in joint_post_2.tsv. I think entries in these two columns are identical. Please correct me if I am wrong.
2. How are the entries in 'cnv_state_post' computed? Do they represent maximum among the columns: p_loh, p_del, p_amp, p_bamp, p_bdel ?

[kzb193]

Hello Dr. Gao,
Can you please help me out with this query?