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NCBI chr reference name different from dbSNP chr names, is that usable by GATK?
I am trying to perform base recalibration on a non-human genome. I've downloaded the dbSNP vcf file from Ensembl (also downloaded another version from NCBI), and for both files the chr naming system is "1, 2, 3...". On the other hand, the NCBI reference file I used named chromosomes differently, chr 1 = gi|966749131|ref|NC_006088.4|, chr2 = gi|966749130|ref|NC_006089.4|...
However, BaseRecalibration seemed to run fine. I am wondering if GATK is capable of internally recognizing the NCBI chromosome names or if their algorithm generated a completely wrong recal table and recalibrated all the scores wrong. I've also attached an output of my AnalyzeCovariates plot in case that helps. Thanks!