Entering edit mode
4.0 years ago
zizigolu
★
4.3k
Hi
I have found a sciclone output via internet like attached
> 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