I have downloaded the databases for dbSNP and COSMIC in order to use the BaseRecalibrator tool in GATK, which has an option called --known-sites. The reference genome I use in GRCh38.p12 from GENCODE (latest version). However, it looks like the indices in my reference genome are "chr1, chr2, chr3 ..... chrX, chrY, chrM", whereas the indices of the variant databases (dbSNP, COSMIC and others) are "1,2,3, .... , X, Y, MT". Due to this, I get an error saying that the indices do not match.
Meanwhile, a few research papers regarding RNA-seq analysis used the same reference genome as mine and also followed GATK's pipeline, using dbSNP and COSMIC databases.
I would like to know if I have to manually manipulate the indices of one of them to make it match or is there any other way.
