Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.

Different results of haplotypecaller using Base Quality Recalibration Score

Dear GATK team,
I have analyzed samples sequenced with an Illumina custom amplicon sequencing kit.
I aligned samples with BWA mem algorithm and then I applied haplotypecaller following the suggestions for hard filtering:


I used two different strategies: with BQRS and without BQRS and I had different results.
In particular using BQRS in two different samples I have 2 variants that are not called by haplotypecaller, I saw them with other callers and they were also validated with Sanger sequencing.
Without the BQRS haplotyecaller is able to detect the variants in both cases.
My question is: Do you have any experience in this kind of problem?
Is there any concerns about using BQRS with amplicon sequencing? Is it better to perform the analysis without BQRS?

Thank you so much,



Sign In or Register to comment.