- New default behavior clears existing QUAL scores. (Use the -q flag to iterate existing QUAL field from input VCF)
- Limit number of reads to 1000 at each variant site (--max_reads), to prevent slow processing time in high-depth, repetitive regions (thanks to brentp)
- add argument (-T) for optional reference FASTA when reading CRAM files. (This prevents automatically downloading of the reference cache)
- Throw error if SVTYPE missing from VCF file