Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.