Hello everyone: I have a problem when using sciclone. I extracted the relevant information needed by sciclone from the vcf file generated from the paired normal tumor data as input, and then the following problem has been encountered. I would like to ask whether a certain screening should be carried out when extracting data from the vcf file? If I need to filter the vcf file, what criteria should I use to filter it? Hope to get your help, thank you very much!

```
[1] "checking input data..."
12462 sites (of 12480 original sites) are copy number neutral and have adequate depth in all samples
0 sites (of 12480 original sites) were removed because of copy-number alterations
18 sites (of 12480 original sites) were removed because of inadequate depth
18 sites (of 12480 original sites) were removed because of copy-number alterations or inadequate depth
[1] "clustering..."
Disable overlapping std dev condition
kmeans initialization:
V1
0.369202574615969
0.0451805969314854
0.0012764317159691
0.068427701248344
0.130563008213922
0.508433685628903
0.419371045057848
0.567150829909654
0.0267695356487535
0.23147262643314
0.998687595233288
0.0133681853132312
0.00484191691530496
0.096954918736847
0.767968455466162
0.306889133938259
0.893953674722921
0.171738804853286
0.647833820706109
0.469620180355922
Using threshold: 0.7
Dropped cluster 5 with too few variants ( 0 ) center: 0.4961276
Dropped cluster 5 with too few variants ( 0 ) center: 0.4889433
Dropped cluster 5 with too few variants ( 0 ) center: 0.4961276
Dropped cluster 7 with too few variants ( 0 ) center: 0.4961276
Dropped cluster 11 with too few variants ( 0 ) center: 0.4961276
Dropped cluster 12 with too few variants ( 0 ) center: 0.4961276
Dropped cluster 12 with too few variants ( 0 ) center: 0.228628
Cluster 1 pi = 0.381 center = 0.382 SEM = (0.372, 0.393) sd = (0.000, 1.000)
Cluster 2 pi = 0.557 center = 0.004 SEM = (0.004, 0.004) sd = (0.000, 0.006)
Cluster 3 pi = 0.062 center = 0.479 SEM = (0.476, 0.482) sd = (0.417, 0.544)
Converged on the following parameters:
mu:
3088.34643978221 88967.680080543 35087.7594185802
alpha:
57064.3763044592 40966.6875698716 574.763038704414
nu:
1720.59558497192 15169.4708677206 33819.9881156314
beta:
19643.4195415117 25.601254166207 510.134678204943
pi:
0.380504889742695 0.557239249326397 0.0622558639309075
[1] "finished clustering full-dimensional data..."
[1] "found 3 clusters using bmm in full dimensional data"
There were 50 or more warnings (use warnings() to see the first 50)
> writeClusterTable(sc, "test.new/clusters1")
> sc.plot1d(sc,"test.new/clusters1.1d.pdf")
>
warnings()
1: did not converge in 10 iterations
2: did not converge in 10 iterations
3: did not converge in 10 iterations
4: did not converge in 10 iterations
5: did not converge in 10 iterations
6: Quick-TRANSfer stage steps exceeded maximum (= 623100)
7: did not converge in 10 iterations
8: did not converge in 10 iterations
9: did not converge in 10 iterations
10: did not converge in 10 iterations
11: did not converge in 10 iterations
12: did not converge in 10 iterations
13: did not converge in 10 iterations
14: did not converge in 10 iterations
15: Quick-TRANSfer stage steps exceeded maximum (= 623100)
16: did not converge in 10 iterations
17: did not converge in 10 iterations
18: Quick-TRANSfer stage steps exceeded maximum (= 623100)
19: Quick-TRANSfer stage steps exceeded maximum (= 623100)
20: Quick-TRANSfer stage steps exceeded maximum (= 623100)
21: did not converge in 10 iterations
22: Quick-TRANSfer stage steps exceeded maximum (= 623100)
23: did not converge in 10 iterations
24: Quick-TRANSfer stage steps exceeded maximum (= 623100)
25: did not converge in 10 iterations
26: did not converge in 10 iterations
27: did not converge in 10 iterations
28: Quick-TRANSfer stage steps exceeded maximum (= 623100)
29: did not converge in 10 iterations
30: did not converge in 10 iterations
31: did not converge in 10 iterations
32: did not converge in 10 iterations
33: did not converge in 10 iterations
34: did not converge in 10 iterations
35: did not converge in 10 iterations
36: did not converge in 10 iterations
37: did not converge in 10 iterations
38: did not converge in 10 iterations
39: did not converge in 10 iterations
40: did not converge in 10 iterations
41: did not converge in 10 iterations
42: did not converge in 10 iterations
43: did not converge in 10 iterations
44: did not converge in 10 iterations
45: Quick-TRANSfer stage steps exceeded maximum (= 623100)
46: did not converge in 10 iterations
47: did not converge in 10 iterations
48: did not converge in 10 iterations
49: did not converge in 10 iterations
50: did not converge in 10 iterations
```

Tagging: Chris Miller