I found this comment that the software currently does not officially support VCF files containing indels. Support for VCFs generated by MuTect 2 that include both single nucleotide variants (SNVs) and indels is planned for Bioconductor 3.5.
Now, the version of bioconductor is 3.5.
So can I classify indel variants as germline vs. somatic with PureCN?
Thanks for your help.