sequenza hg38 bins and blacklists

[Heather Grant]

Dear group, 

I am a new user trying to use sequenza with hg38. I have had luck with the Sequenza_CNAqc() function in CNAqc which gives hg38 as an option. I have two questions: 

1. Does sequenza give segments in bins? At the moment it is giving segments to the nearest base pair and finding teeny tiny segments. I have specified w -50 in the seqz_binning step but it doesn't seem to come through. A Nextflow pipeline I previously used also gives answers to the nearest base pair (so I don't think that's a CNAqc quirk?) 

2. Is there a blacklist for hg38 being used automatically? It seems the beginning of chr 13, 14,15 is being blacklisted, but where is this information? Can you specify additional blacklist bins? There are some streaks the depth ratio that look concerning. 

Thank you, 

Heather