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!
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$\begingroup$ 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. $\endgroup$– terdon ♦Nov 4, 2019 at 11:00
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2 Answers
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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.
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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.
