Hi

I have found a sciclone output via internet like attached

sciclone_out.txt

> head(sciclone_out[1:2,])
  chr        st Time_1.ref Time_1.var Time_1.vaf Time_1.cn Time_1.cleancn
1   1 160771583       8788       6182   41.29593         2              2
3   1 220276043       4557       3464   43.18664         2              2
  Time_1.depth Time_2.ref Time_2.var Time_2.vaf Time_2.cn Time_2.cleancn
1        14970       8606          9 0.10446895         2              2
3         8021      22588         19 0.08404476         2              2
  Time_2.depth Time_3.ref Time_3.var Time_3.vaf Time_3.cn Time_3.cleancn
1         8615       6938       3137   31.13648         2              2
3        22607       2406       1108   31.53102         2              2
  Time_3.depth Time_4.ref Time_4.var Time_4.vaf Time_4.cn Time_4.cleancn
1        10075      10541         10 0.09477775         2              2
3         3514      13074          9 0.06879156         2              2
  Time_4.depth Time_5.ref Time_5.var Time_5.vaf Time_5.cn Time_5.cleancn
1        10551       6684        700   9.479957         2              2
3        13083       3161        422  11.777840         2              2
  Time_5.depth adequateDepth cluster cluster.prob.1 cluster.prob.2 cluster.prob.3
1         7384             1       1              1          1e-09          1e-09
3         3583             1       1              1          1e-09          1e-09
  cluster.prob.4 gene_name   Time_1     Time_2   Time_3     Time_4    Time_5
1          1e-09       LY9 41.29593 0.10446895 31.13648 0.09477775  9.479957
3          1e-09     IARS2 43.18664 0.08404476 31.53102 0.06879156 11.777840
>

From this data, how I know if variants in a given cluster let's say cluster 1 is clonal or sub-clonal?

I have two groups of patients and my goal is comparing the number of clonal and sub-clonal variants between them or may be further connection sub-clonal fraction to clinal data

Here we have clustered VAF but I can not figure out how to say if a genes having a variant in a cluster is clonal or sub-clonal

Can you help me?

Thanks