Since 2014, I specifically focus on the development of tools dedicated to improve the analyses of Next Generation Sequencing applications (WES/WGS).
In particular, I have developped and published:

• AnnotSV: a tool designed to annotate, rank and prioritize Structural Variations
• VaRank: a tool designed to annotate, rank and prioritize SNV/indel from NGS data

Background: Structural Variations (SV) are a major source of variability in the human genome that shaped its actual structure during evolution. Moreover, many human diseases are caused by SV, highlighting the need to accurately detect those genomic events but also to annotate them and assist their biological interpretation.

Results: We developed AnnotSV that compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to (i) interpret SV potential pathogenicity and (ii) filter out SV potential false positive.

AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis.
Geoffroy V, Guignard T, Kress A, Gaillard JB, Solli-Nowlan T, Schalk A, Gatinois V, Dollfus H, Scheidecker S, Muller J.
NAR. 2021 May 22. doi: 10.1093/nar/gkab402

AnnotSV: An integrated tool for Structural Variations annotation.
Geoffroy V, Herenger Y, Kress A, Stoetzel C, Piton A, Dollfus H, Muller J.
Bioinformatics. 2018 Apr 14. doi: 10.1093/bioinformatics/bty304

Background: Most genetic disorders are caused by single nucleotide variations (SNVs) or small insertion/deletions (indels). High throughput sequencing has broadened the catalogue of human variation, including common polymorphisms, rare variations or disease causing mutations. However, identifying one variation among hundreds or thousands of others is still a complex task for biologists, geneticists and clinicians.

Results: We have developed VaRank, a command-line tool for the ranking of genetic variants detected by high-throughput sequencing. VaRank scores and prioritizes variants annotated either by Alamut Batch or SnpEff. A barcode allows users to quickly view the presence/absence of variants (with homozygote/heterozygote status) in analyzed samples. VaRank supports the commonly used VCF input format for variants analysis thus allowing it to be easily integrated into NGS bioinformatics analysis pipelines. VaRank has been successfully applied to disease-gene identification as well as to molecular diagnostics setup for several hundred patients.

VaRank: a simple and powerful tool for ranking genetic variants.
Geoffroy V, Pizot C, Redin C, Piton A, Vasli N, Stoetzel C, Blavier A, Laporte J, Muller J.
PeerJ. 2015. doi: 10.7717/peerj.796