I have the following questions regarding sciClone and whole-exome sequencing data:
- Can it be used for exome sequencing data (and did someone manage to use it with WES and got decent results?)
- Should I make special considerations when making the VAF file from my exome sequencing results, like criteria for variant selection and so on
- Which tool can be used for best copy number prediction on exome seq data. My samples have both normal and tumor.