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Old 11-01-2016, 04:00 AM   #2
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Location: Bethesda MD

Join Date: Oct 2009
Posts: 505

A few possible explanations:

1) higher error rate in the sequence data from the TruSeq sample, producing false-positive variant calls. You can use FastQC to assess the base quality metrics of the two data sets.

2) capture of highly polymorphic loci in the TruSeq but not Nextera enrichment. Compare the covered intervals with Bedtools, and see if there's a large difference in variant frequency between the shared vs unique regions.
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