PT  - JOURNAL ARTICLE
AU  - Ruining Dong
AU  - Daniel Cameron
AU  - Justin Bedo
AU  - Anthony T Papenfuss
TI  - svaRetro and svaNUMT: Modular packages for annotation of retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
AID  - 10.1101/2021.08.18.456578
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.08.18.456578
4099  - http://biorxiv.org/content/early/2021/08/19/2021.08.18.456578.short
4100  - http://biorxiv.org/content/early/2021/08/19/2021.08.18.456578.full
AB  - Background The biological significance of structural variation is now more widely recognized. However, due to the lack of available tools for downstream analysis, including processing and annotating, interpretation of structural variant calls remains a challenge.Findings Here we present svaRetro and svaNUMT, R packages that provide functions for annotating novel genomic events such as non-reference retro-copied transcripts and nuclear integration of mitochondrial DNA. We evaluate the performance of these packages to detect events using simulations and public benchmarking datasets, and annotate processed transcripts in a public structural variant database.Conclusions svaRetro and svaNUMT provide efficient, modular tools for downstream identification and annotation of structural variant calls.Competing Interest StatementThe authors have declared no competing interest.SVstructural variantNUMTnuclear mitochondrial integrationRTretroposed transcriptTSDtarget site duplicationmtDNAmitochondrial DNA