The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
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.