From Fastq to vcf

Question

[yakko]

Hi, While calling variants the last suggested step from gatk is the Recalibration. What should I expect without this filter? Thanks.

[gb]

While I am pretty sure I can't answer that question for you, you may consider to change the title of your post. It does not really match your actual question now.

Did you also found this page already? https://gatk.broadinstitute.org/hc/en-us/articles/360035890531-Base-Quality-Score-Recalibration-BQSR-

Answer 1

[MatthewP]

Hello, this post from GATK suggest hard-filtering.