Skip to Main content Skip to Navigation
Poster communications

SVJedi-graph: Structural Variant genotyping with long-reads using a variation graph

Sandra Romain 1 Claire Lemaitre 1
1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : Structural variants (SVs) are genomic segments of more than 50 bp that have been rearranged in the genome. The advent of third generation sequencing technologies has increased and enhanced their study, and a great number of SVs has already been discovered in the human genome. Complementary to their discovery, the genotyping of known SVs in newly sequenced individuals is of particular interest for several applications such as trait association and clinical diagnosis. Most of the SV genotypers currently available are designed for second generation sequencing data, although third generation sequencing data is more suited to study SVs due to their large range of sizes (up to few mega bases). As such, our team previously released SVJedi, the first SV genotyper dedicated to long read data[1]. The method is based on linear representations of the allelic sequences of each SV and each SV is represented and genotyped independently of the other ones. While this is very efficient for distant SVs, the method fails to genotype some closely located or overlapping SVs due to redundancy in representative allelic sequences.
Document type :
Poster communications
Complete list of metadata

https://hal.inria.fr/hal-03441915
Contributor : Claire Lemaitre Connect in order to contact the contributor
Submitted on : Monday, November 22, 2021 - 8:43:57 PM
Last modification on : Thursday, November 25, 2021 - 3:13:15 AM

File

JOBIM2021_paper_117.pdf
Files produced by the author(s)

Identifiers

  • HAL Id : hal-03441915, version 1

Citation

Sandra Romain, Claire Lemaitre. SVJedi-graph: Structural Variant genotyping with long-reads using a variation graph. JOBIM 2021, Jul 2021, Paris, France. ⟨hal-03441915⟩

Share

Metrics

Record views

4

Files downloads

18