Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-04T10:04:46.443Z
Answers.LastActivityDate: 2019-11-05T14:09:20.417Z
Answers.LastEditDate: 2019-11-05T14:09:20.417Z
Answers.UserDisplayName: Graeme
Answers.Body: <p>For your negative controls, you might want to check out QC Fail (<a href="https://sequencing.qcfail.com/" rel="nofollow noreferrer">https://sequencing.qcfail.com/</a>).  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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-04T10:21:49.393Z
Answers.LastActivityDate: 2019-11-04T10:21:49.393Z
Answers.UserDisplayName: Jay Moore
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-04T11:00:36.017Z
Comments.Text: Hi and welcome to the site! Could you please [edit] your question and narrow it down a little. We don't do discussions here, we're strictly Questions and Answers, so the more specific the question, the better. What parameters are you interested in? GC content? Coverage? FASTQ quality? Insert size distribution? What will the sequences be used for (different applications may need different approaches). Please narrow the scope of your question down.
Comments.UserDisplayName: terdon
Tags: <wgs><qc>
Title: Common QC parameters and threshold in human WGS pipeline
ThreadText: # Common QC parameters and threshold in human WGS pipeline
  
  (Asked by: username_0 on 2019-11-04)
  
  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!
  
  **Tags:** wgs, qc
  
  > **Comments:**
  > **username_1**: Hi and welcome to the site! Could you please [edit] your question and narrow it down a little. We don't do discussions here, we're strictly Questions and Answers, so the more specific the question, the better. What parameters are you interested in? GC content? Coverage? FASTQ quality? Insert size distribution? What will the sequences be used for (different applications may need different approaches). Please narrow the scope of your question down.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2019-11-04. Score: 2
  
  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.
  
  
  ---
  
  ### Answer by username_3 on 2019-11-04. Score: 0
  
  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.
  
  
  ---
  
  