Open Parsoa opened 3 years ago
Hi Parsoa,
I think if you use the database file for PacBio (hg19_selected_VNTRs_Pacbio.db) instead of hg38_selected_VNTRs_Illumina.db it will work. It has other loci that works with --pacbio
which don't exist in hg38_selected_VNTRs_Illumina.db.
We haven't tested adVNTR using PacBio reads on GRCh38 and while it should work, we don't have test data or models for it. Let me know if you specifically have GRCh38 data and I can look into how to make it work.
I tried with the hg19_selected_VNTRs_Pacbio.db
too but I still get the same error (anyway I'm not sure if this would have worked as my sample is mapped th hg38). I get the same error even if I don't pass --models
.
Hi Mehrdad,
I'm trying to run advntr on some PacBio reads mapped to hg38 and I'm using the hg38 models (hg38_selected_VNTRs_Illumina.db) however I get a
sqlite3.OperationalError
when running with the following options:All the files referenced in the command exist. I tried redownloading the VNTR models in case they were corrupted. I get the same error if I use the hg19 ones. Any suggestions? Thanks.