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?
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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.
For your negative controls, you might want to check out QC Fail (https://sequencing.qcfail.com/). There you can see examples of how things look in QC when things have gone wrong, such as loss of quality, position-specific errors on flowcells and contamination with primer dimers.