FilterFFPE-package {FilterFFPE} | R Documentation |
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.
Package: | FilterFFPE |
Type: | Package |
Title: | FFPE Artificial Chimeric Read Filter for NGS data |
Version: | 1.3.0 |
Authors@R: | person("Lanying", "Wei", email="lanying.wei@uni-muenster.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4281-8017")) |
Description: | 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. |
License: | LGPL-3 |
Encoding: | UTF-8 |
Imports: | foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors |
Suggests: | BiocStyle |
biocViews: | StructuralVariation, Sequencing, Alignment, QualityControl, Preprocessing |
git_url: | https://git.bioconductor.org/packages/FilterFFPE |
git_branch: | master |
git_last_commit: | 7608296 |
git_last_commit_date: | 2021-05-19 |
Date/Publication: | 2021-06-03 |
Author: | Lanying Wei [aut, cre] (<https://orcid.org/0000-0002-4281-8017>) |
Maintainer: | Lanying Wei <lanying.wei@uni-muenster.de> |
The next-generation sequencing (NGS) reads from formalin-fixed paraffin-embedded (FFPE) samples contain numerous artifact chimeric reads, which can lead to a large number of false positive structural variation (SV) calls. This package finds and filters these artifact chimeric reads from BAM files of FFPE samples to improve SV calling performance.
Index of help topics:
FFPEReadFilter Find and filter artifact chimeric reads in BAM file of FFPE sample FilterFFPE-package FFPE Artificial Chimeric Read Filter for NGS data filterBamByReadNames Filter reads from BAM file by read names findArtifactChimericReads Find artifact chimeric reads in BAM file of FFPE sample
There are three available functions to find and/or filter artifact chimeric reads of FFPE samples:
1. findArtifactChimericReads
: Find artifact chimeric reads in BAM
file of FFPE sample.
2. filterBamByReadNames
: Filter reads from BAM file by read names.
3. FFPEReadFilter
: Find and filter artifact chimeric reads in BAM
file of FFPE sample.
Lanying Wei <lanying.wei@uni-muenster.de>
FilterFFPE
, filterBamByReadNames
,
FFPEReadFilter
file <- system.file("extdata", "example.bam", package = "FilterFFPE") outFolder <- tempdir() FFPEReadsFile <- paste0(outFolder, "/example.FFPEReads.txt") dupChimFile <- paste0(outFolder, "/example.dupChim.txt") destination <- paste0(outFolder, "/example.FilterFFPE.bam") FFPEReadFilter(file = file, threads = 2, destination = destination, overwrite = TRUE, FFPEReadsFile = FFPEReadsFile, dupChimFile = dupChimFile)