ngs MiSeq pipeline vs GATK best practices

0

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


pipeline


gatk


MiSeq


ngs

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