Open maxmilianr opened 6 months ago
Hi,
our variant catalog contains OfftargetRegions on alternate contigs, e.g. "chr4_KI270790v1_alt:200469-201085"
ExpansionHunter works without issues and i get a valid vcf-file.
When starting REviewer with the exact same assembly reference and catalog, i get the error:
[error] Invalid contig name chr4_KI270790v1_alt
Removing all alt. contigs from the catalog results in the error: [error] Failed to extract reads from the specified region
[error] Failed to extract reads from the specified region
This is the catalog file: variant_catalog_gnomAD_with_offtargets.GRCh38_202306.json
Hi,
our variant catalog contains OfftargetRegions on alternate contigs, e.g. "chr4_KI270790v1_alt:200469-201085"
ExpansionHunter works without issues and i get a valid vcf-file.
When starting REviewer with the exact same assembly reference and catalog, i get the error:
[error] Invalid contig name chr4_KI270790v1_altRemoving all alt. contigs from the catalog results in the error:
[error] Failed to extract reads from the specified regionThis is the catalog file: variant_catalog_gnomAD_with_offtargets.GRCh38_202306.json