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Quality Score Re-calibration without dbSNP
As I know GATK SNP calling involve the following steps:
1. Base-calling and image analysis
Last step of Alignment is Quality score re-calibration which include Count covariates and table re-calibration.
Can I know how to Quality Score Re-calibration if I don't have dbSNP for my query sequence?
My sequence is newly assembly transcriptome.
Thus I don't have any suitable dbSNP for it.
Or I can just stop at "Local realignment around indels" and continue into SNP-calling for newly sequenced transcriptome?
Thanks and looking forward to hear from you.