GATK QC where I start?

Question

[ManuelDB]

I am in a clinical training program working in a genomics lab. I am becoming familiar with the NGS pipeline. One of the competencies is quality control. In the GATK Tool Documentation Index, the list of tools for QC is extensive. I was wondering which of them are normally used in clinical settings or what are the most appropriate tools to evaluate the quality of the data in the different steps of the NGS workflow.

I am new in this field so any recommendation would be welcome.

[raphael.B]

A 'classic' starting point could be the Variant Quality Score Recalibration (VQSR). You can also take a look at hard filtering guidelines that detail quite well few useful metrics for variant QC (hard filters).