ngs MiSeq pipeline vs GATK best practices

Question

[tinakopale]

Hi,

I am working with WES data and I am trying to build a pipeline with the help of GATK best practices. I would like to know the difference between pipeline that is built-in in Illumina sequencer and GATk Best Practices pipeline.

Is the VQSR used in built in software of Illumina? Why should I follow Best practices when everything is built in sequencer, can you please help me to see the difference?

Thank you very much

[h.mon]

If the pipeline built-in in Illumina sequencers you are refering to is the DRAGEN pipeline, then there aren't many differences, and the plan is for them to be the same:

DRAGEN-GATK Update: Let's get more specific

The hardware-accelerated DRAGEN pipeline found in Illumina sequencers is subscription-based, but a lot faster, so it may suit the needs of big sequencing centers and service providers.

[tadeja.klade]

Thank you, it is not the Dragan pipeline that is built-in.