3 comments on ““You should definitely not run base quality score recalibration without a dbSNP reference”

  1. I came across that thread earlier today as well. I am working on a bacterial genome…which of course dbSNP has no record of =) I had my suspensions that I should skip the re-cal part, and the thread confirmed my thoughts. I saw people also suggested trying Variant quality score recalibration (also in GATK) after variant calling. Have you tried it? Any comments are appreciated! =)

  2. Well, my long answer just disappeared. Yes, it needs confident SNPs to set a calibration standard. So if you do not have one, it may not be possible. I think if read depth is >30 then BQSR is not necessary.
    I will write a new entry on how I am cleaning up SNP data when depth is >30-40 and sample size >100.

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