local realignment file

[j-knome]

Hi, I'm curious if VarDict generates a file that documents its local realignment processes. Specifically, in instances where VarDict identifies longer indels (exceeding 50 base pairs), there have been observed cases where the supporting reads for these longer insertions do not encompass the entire predicted variant. I'm inquiring if there are any available methods or options within VarDict to generate a file that records these local realignments. Such a file would be instrumental in troubleshooting situations where VarDict predicts extended variants that are not entirely represented by the sequences found in the supporting reads, which VarDict relies upon to make these calls.