License
when quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2018.4
URN: urn:nbn:de:0030-drops-93060
URL: http://drops.dagstuhl.de/opus/volltexte/2018/9306/

Sirén, Jouni ; Garrison, Erik ; Novak, Adam M. ; Paten, Benedict J. ; Durbin, Richard

Haplotype-aware graph indexes

pdf-format:
Dokument 1.pdf (651 KB)


Abstract

The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true haplotypes. We augment the VG model with haplotype information to identify which paths are more likely to be correct. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows-Wheeler transform. We demonstrate the scalability of the new implementation by indexing the 1000 Genomes Project haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.

BibTeX - Entry

@InProceedings{sirn_et_al:LIPIcs:2018:9306,
  author =	{Jouni Sir{\'e}n and Erik Garrison and Adam M. Novak and Benedict J. Paten and Richard Durbin},
  title =	{{Haplotype-aware graph indexes}},
  booktitle =	{18th International Workshop on Algorithms in  Bioinformatics (WABI 2018)},
  pages =	{4:1--4:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Laxmi Parida and Esko Ukkonen},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2018/9306},
  URN =		{urn:nbn:de:0030-drops-93060},
  doi =		{10.4230/LIPIcs.WABI.2018.4},
  annote =	{Keywords: FM-indexes, variation graphs, haplotypes}
}

Keywords: FM-indexes, variation graphs, haplotypes
Seminar: 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Issue date: 2018
Date of publication: 26.07.2018


DROPS-Home | Fulltext Search | Imprint | Privacy Published by LZI