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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

Question about BQSR


I am trying to figure something out in GATK, namely, BQSR. I am working an organism for which there are no known SNPs, so I ran the haplotype caller on uncalibrated data (realigned_reads.bam and raw_variants.vcf). Then I ran BQSR using the raw_variants.vcf file as the knownSites. According to my understanding, since the BQSR would SKIP re-calibrating SNPs from the knownSites file, the qualities for this variant in the before file (realigned_reads.bam) should be the same after re-calibration (recal_reads.bam). But as you can see from the color of the nucleotides, they are indeed lower QS (much lower) after recalibration. This is the source of my confusion. According to the docs, this site should have been skipped. Any clarification would be greatly appreciated.

Thank you.


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