text: user6449: 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!
  
  user3100: 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.
  
original_text: 6449: <p>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.</p>
  
  <p>Which qc parameters for WGS are you using and why?</p>
  
  <p>Thanks!</p>
   3100: <p>I would suggest you look at the website for the excellent MultiQC tool (<a href="https://multiqc.info/" rel="nofollow noreferrer">https://multiqc.info/</a>).  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.</p>
  
  <p>If you dig around in their GitHub repo (<a href="https://multiqc.info/" rel="nofollow noreferrer">https://multiqc.info/</a>) 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.</p>
  