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appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV

Bioconductor version: Release (3.19)

The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.

Author: Sarah Sandmann

Maintainer: Sarah Sandmann <sarah.sandmann at>

Citation (from within R, enter citation("appreci8R")):


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

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


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:

Using appreci8R PDF R Script
Reference Manual PDF


biocViews GeneticVariability, SNP, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.22.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License LGPL-3
Imports shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment
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Follow Installation instructions to use this package in your R session.

Source Package appreci8R_1.22.0.tar.gz
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macOS Binary (x86_64) appreci8R_1.22.0.tgz
macOS Binary (arm64) appreci8R_1.22.0.tgz
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Source Repository (Developer Access) git clone
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