Registration and Call for Abstracts Open for Bioc2024


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

FFPE Artificial Chimeric Read Filter for NGS data

Bioconductor version: Development (3.19)

This package finds and filters artificial chimeric reads specifically generated in next-generation sequencing (NGS) process of formalin-fixed paraffin-embedded (FFPE) tissues. These artificial chimeric reads can lead to a large number of false positive structural variation (SV) calls. The required input is an indexed BAM file of a FFPE sample.

Author: Lanying Wei [aut, cre]

Maintainer: Lanying Wei <lanying.wei at>

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


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:

An introduction to FilterFFPE PDF R Script
Reference Manual PDF


biocViews Alignment, Preprocessing, QualityControl, Sequencing, Software, StructuralVariation
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License LGPL-3
Imports foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors
System Requirements
See More
Suggests BiocStyle
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package FilterFFPE_1.13.0.tar.gz
Windows Binary
macOS Binary (x86_64) FilterFFPE_1.13.0.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats