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.

How to interpret a very broad distribution of QUAL

Dear GATK team,

We applied the best practice DNA-seq pipeline and generated SNP/indel variant calls from targeted sequencing of 700Kb in 500 samples.

According to this GATK post, the typical QUAL score ranges between 2 to 63.
https://www.broadinstitute.org/gatk/guide/tagged?tag=quality-scores

We looked at "PASS" variants/sites and found that the distribution of QUAL in our data is very broad with min=30, median=6195, max=10M. Is is distribution normal or an indication of abnormality of this callset? If this is abnormal, what should we be looking at for trouble shoot?

We note that the concordance between genotypes from our targeted sequencing and known genotypes in the same samples are >99% - seems satisfactory.

Thanks in advance.

Jin

Best Answer

Answers

Sign In or Register to comment.