allelic copy number variation

Question

[Bogdan]

Dear all,

I am working with sequenza output that has the following format - 1st line (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269342/ ; Sequenza estimates the allelic specific copy numbers). How can I transform this output into numerical allele specific copy-numbers shown on the 2nd line ?

chromosome  position    base.ref    depth.normal    depth.tumor depth.ratio Af  Bf  zygosity.normal GC.percent  good.reads  AB.normal   AB.tumor    tumor.strand
chr1    12975   N   7   20  2.841   1   0   hom 60  51  N   .   0

The output needs to be as :

Chromosome Start_position End_position total_cn A_cn B_cn      
chr1 14574       952448        5    0    5

Thanks so much,

Bogdan