base re-calibration when I don't have a publicly available dbSNP
I want to perform base re-calibration using BaseRecalibrator. However, I work on a non-model organism and there is no available SNP database.
Would it be right way if I creat my custom dbSNP file using very stringent criteria (--min_base_quality_score 30) for SNP calling and re-calibrate my data using this file?
I also wonder if I will benefit from re-calibration when I use custom dbSNP.vcf, which is produced from the same samples I analyze?
I create dbSNP.vcf using UnifiedGenotyper to save time, while for genotyping after base re-calibration I use HaplotypeCaller. I have 24 samples in this analysis.
I would appreciate your assistance.