What is the Dragen filtering rule based on QUAL?
How do I filter variants produced by the GATK DRAGEN model?
It was stated in the GATK 4.2 blog announcement that the DRAGEN has a very simple hard-filtering rule based on the QUAL score only.
What is the very simple filter rule? So is the previous VQSR step no longer required?
DRAGEN does hard filtering on QUAL, filtering below a QUAL of 10.41. The DRAGEN-GATK method will output very similar QUAL scores to DRAGEN and will also recommend hard filtering on QUAL, though we don't have our specific filtering rule published yet.
The first release of the DRAGEN-GATK pipeline will be focused on the best practices for single sample analysis. The filtering method on QUAL will replace VQSR for this best practices. VQSR will still be relevant for the joint calling best practices, because we will not use the new DRAGEN-GATK method for joint calling in our first release.
Hope this helps to clarify,
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