I tried to use sciClone on test data prior to applying any script on my actual patient database, but the program persistently keeps returning the following error message;
 "checking input data..."  "No copy number files specified.
Assuming all variants have a CN of
2."  "ERROR: column vaf in sample 5 is not numeric" Error in cleanAndAddCN(vafs[[i]], copyNumberCalls[[i]], i,cnCallsAreLog2, :
I've only tried entering SNP data as my database contains mainly SNVs stemming from targeted sequencing on specific gene panels. Below you can download the test files as well as view the actual script that I tried to run