Rxivist logo

SVJedi: Genotyping structural variations with long reads

By Lolita Lecompte, Pierre Peterlongo, Dominique LAVENIER, Claire Lemaitre

Posted 21 Nov 2019
bioRxiv DOI: 10.1101/849208 (published DOI: 10.1093/bioinformatics/btaa527)

Motivation Studies on structural variants (SV) are expanding rapidly. As a result, and thanks to third generation sequencing technologies, the number of discovered SVs is increasing, especially in the human genome. At the same time, for several applications such as clinical diagnoses, it is important to genotype newly sequenced individuals on well defined and characterized SVs. Whereas several SV genotypers have been developed for short read data, there is a lack of such dedicated tool to assess whether known SVs are present or not in a new long read sequenced sample, such as the one produced by Pacific Biosciences or Oxford Nanopore Technologies. Results We present a novel method to genotype known SVs from long read sequencing data. The method is based on the generation of a set of reference sequences that represent the two alleles of each structural variant. Long reads are aligned to these reference sequences. Alignments are then analyzed and filtered out to keep only informative ones, to quantify and estimate the presence of each SV allele and the allele frequencies. We provide an implementation of the method, SVJedi, to genotype insertions and deletions with long reads. The tool has been applied to both simulated and real human datasets and achieves high genotyping accuracy. We also demonstrate that SV genotyping is considerably improved with SVJedi compared to other approaches, namely SV discovery and short read SV genotyping approaches. Availability <https://github.com/llecompte/SVJedi.git> Contact lolita.lecompte{at}inria.fr

Download data

  • Downloaded 592 times
  • Download rankings, all-time:
    • Site-wide: 30,462 out of 106,159
    • In bioinformatics: 3,988 out of 9,474
  • Year to date:
    • Site-wide: 13,580 out of 106,159
  • Since beginning of last month:
    • Site-wide: 36,298 out of 106,159

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News