SCAN2 for "clonal" sSNVs?

[proukakis]

hello, i appreciate the logic for not reporting any mutations with supporting reads in bulk WGS, but this probably is redundant if there is matched high coverage bulk genome eg 100x WGS- even low clonal mutations might have supporting reads. Could there be an option to report separately the single cell putative sSNVs with a low number of matching bulk reads, (to be set manually)? Thanks

[jluquette]

Hi @proukakis,

We are indeed working on allowing the user to relax the bulk filter (i.e., currently 0 mutation supporting reads in bulk are tolerated; options to increase this by count or by VAF in bulk are being added).

The tricky part isn't changing those bulk filters, but rather re-assessing the tool's performance. We don't know how many false positives (either artifacts that bulks help to remove or germline mutations) will be included if the bulk filter is relaxed.