Common QC parameters and threshold in human WGS pipeline I am trying to summarize a list of QC-parameters and its threshold that should be applied for human WGS in general to avoid bad quality of data.

Which qc parameters for WGS are you using and why?

Thanks!
I would suggest you look at the website for the excellent MultiQC tool (https://multiqc.info/).  We use it in a clinical setting to collate all the QC statistics from our pipelines into a single report (It displays results from multiple QC programs such as FastQC, Picard, bcl2fastq, VerifyBAMid etc).  The homepage has a selection of example reports - clicking on "Whole Genome Seq" shows a report with the metrics most labs would expect from their WGS pipeline.

If you dig around in their GitHub repo (https://multiqc.info/) you will get a good idea of the default thresholds set for flagging results - there should be a config file somewhere specifying all these values.