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Identical by descent tracts in unphased genotypes

Description

Abstract:
I am designing a program to be able to identify Identical by Descent (IBD) tracts in unphased genotypes. In many cases, when genomes are sequenced, it can be difficult to localize which fragments of known sequence belong on which of a set of complimentary chromosomes, and as such, sequence data can be ambiguous. Usually this ambiguity is resolved through phasing, where the each piece of known sequence is localized to one particular complimentary chromosome via statistical estimates and knowledge of relationships between sequences. Once done, it is possible to determine if two portions of DNA sequence in two separate chromosomes share a common ancestral origin. However, the common ancestral origin information (a.k.a. Identical By Descent) would be very useful for the statistics involved in phasing, thus the ability to determine the tracts of Identical by Descent DNA sequence would assist the statistical accuracy of the phasing if it could be done first. That is what my program currently aims to accomplish, as efficiently in both time and memory possible.

Citation

Seidman, Daniel, "Identical by descent tracts in unphased genotypes" (2015). Summer Research Symposium. Brown Digital Repository. Brown University Library. https://doi.org/10.26300/zsqr-4b69

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Collection:

  • Summer Research Symposium

    Each year, Brown University showcases the research of its undergraduates at the Summer Research Symposium. More than half of the student-researchers are UTRA recipients, while others receive funding from a variety of Brown-administered and national programs and fellowships and go …
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