Questions about the calculation of CCF

[huerqiang]

Hi, thank you very much for your greate package! I have some questions about how to calculate CCF:
(1) We I only have total copy number, I set up minor_cn = 0 and major_cn = toltal copy number as you describe in #19. I would like to ask the details of the calculation whether half of the total copy number will be automatically assigned to minor_cn and major_cn?
(2) I found that the current version of pyclone-vi provides only the CCF value of the cluster, not the CCF value of each mutation. May I ask if the CCF value of cluster is the average of all the CCF values in the clsuter?
(3) I got my vcf file from Mutect2, and the file is simply read as follows:

> head(vcf)
    V1     V2                           V9                                                        V10
1 chr1  69511 GT:AD:AF:DP:F1R2:F2R1:FAD:SB          0/1:0,480:0.997:480:0,175:0,145:0,327:0,0,275,205
2 chr1 930314 GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/1:288,246:0.448:534:121,97:86,71:212,172:139,149,117,129
3 chr1 941119 GT:AD:AF:DP:F1R2:F2R1:FAD:SB             0/1:0,226:0.994:226:0,97:0,52:0,156:0,0,137,89
4 chr1 942382 GT:AD:AF:DP:F1R2:F2R1:FAD:SB             0/1:115,10:0.056:125:28,3:25,0:96,5:38,77,10,0
5 chr1 942383 GT:AD:AF:DP:F1R2:F2R1:FAD:SB               0/1:120,3:0.03:123:26,0:25,0:100,3:44,76,3,0
6 chr1 942391 GT:AD:AF:DP:F1R2:F2R1:FAD:SB            0/1:132,11:0.063:143:32,3:28,1:106,8:42,90,10,1

Could I use the AF value as VAF value? And I found that a large number of AF values are greater than 0.5, and the CCF values calculated from them may be greater than 1. Are these normal?