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This is the development version of svaNUMT; for the stable release version, see svaNUMT.

NUMT detection from structural variant calls

Bioconductor version: Development (3.20)

svaNUMT contains functions for detecting NUMT events from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion sites found on the nuclear genome within a certain distance threshold. The candidate NUMTs are reported by events.

Author: Ruining Dong [aut, cre]

Maintainer: Ruining Dong <lnyidrn at>

Citation (from within R, enter citation("svaNUMT")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

svaNUMT Package HTML R Script
Reference Manual PDF


biocViews Annotation, DataImport, Genetics, Sequencing, Software, VariantAnnotation
Version 1.11.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3 + file LICENSE
Depends GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0)
Imports assertthat, stringr, dplyr, methods, rlang, GenomeInfoDb, S4Vectors, GenomicFeatures, pwalign
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Suggests TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown
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Source Package svaNUMT_1.11.0.tar.gz
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