Open lkhilton opened 1 year ago
@HoumanLM Could your new indexing approach using the RSamtools package help us resolve this?
@rdmorin For the tabix part that we have discussed earlier, I used Rsamtools for having a function similar to 'get_ssm_by_region' so it seems that it can solve the issue.
I haven't fully debugged this, but I've been trying to retrieve variants for a small aSHM region. It works for genomes, but not capture:
I believe the capture maf file doesn't have any rows matching the region described by
regions$regions[2]
so vroom is choking on the specified column types. Can you please investigate? Ideally this would be robust to even small regions where one might find no mutations.