RT Journal Article
SR Electronic
T1 svaRetro and svaNUMT: Modular packages for annotation of retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.08.18.456578
DO 10.1101/2021.08.18.456578
A1 Ruining Dong
A1 Daniel Cameron
A1 Justin Bedo
A1 Anthony T Papenfuss
YR 2021
UL http://biorxiv.org/content/early/2021/08/19/2021.08.18.456578.abstract
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