Entering edit mode
2.0 years ago
chimerajit
•
0
I am Using GATK on Oryza samples and used NCBI Reference and annotation "GCF_001433935.1_IRGSP-1.0_genomic.fna" I searched and found ENA have known site vcf for the same GCA_001433935.1_current_ids.vcf . However, when I used them for BQSR they are not compatible.
I like to know where can I get known variant VCF which compatible to NCBI reference?
This file likely doesn't exist. GATK to my knowledge has mostly been used on human data, though there is now a bacterial analysis suite as well.