Parentage assignment with genotyping‐by‐sequencing data

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Abstract
In this paper, we evaluate using genotype‐by‐sequencing (GBS) data to perform parentage assignment in lieu of traditional array data. The use of GBS data raises two issues: First, for low‐coverage (e.g., 2×) GBS data performs similarly to array data and requires only a small number of markers to correctly assign parents and (b) low‐coverage GBS data (as low as 0.1×) can also be used, provided that it is obtained across a large number of markers. When analysing the low‐coverage GBS data, we also found a high number of false positives if the true parent is not contained within the list of candidate parents, but that this false positive rate can be greatly reduced by hand tuning the assignment threshold. We provide this parentage assignment method as a standalone program called AlphaAssign.
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Funding Information
  • Biotechnology and Biological Sciences Research Council (BB/J004235/1, BB/L020467/1, BB/L020726/1, BB/M009254/1, BB/N004728/1, BB/N004736/1, BB/N006178/1)
  • Medical Research Council (MR/M000370/1)

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