Dear Chris, I tried using the integration of clonevol and sciclone (RUN) script. After infer.clonal.models I get

```
Sample 1: Tumor <-- Tumor
Sample 2: Relapse <-- Relapse
Using monoclonal model
Note: all VAFs were divided by 100 to convert from percentage to proportion.
Generating non-parametric boostrap samples...
Tumor : Enumerating clonal architectures...
Determining if cluster VAF is significantly positive...
Exluding clusters whose VAF < min.cluster.vaf=0.01
Non-positive VAF clusters:
Tumor : 76 clonal architecture model(s) found
Relapse : Enumerating clonal architectures...
Determining if cluster VAF is significantly positive...
Exluding clusters whose VAF < min.cluster.vaf=0.01
Non-positive VAF clusters: 4,6
Relapse : 2 clonal architecture model(s) found
Finding consensus models across samples...
Found 0 consensus model(s)
Found 0 consensus model(s)
Scoring models...
Pruning consensus clonal evolution trees....
Seeding aware pruning is: off
Number of unique pruned consensus trees: 0
```

and then I get

```
f = generateFishplotInputs(results=res)
Error in 1:nrow(results$matched$index) : argument of length 0
```

Is it because there is no consensus models found between the two samples (tumor and relapse?

Best Mo

Tagging: Chris Miller