FilterFFPE-package: FFPE Artificial Chimeric Read Filter for NGS data
In LanyingWei/FilterFFPE: FFPE Artificial Chimeric Read Filter for NGS data

Description Details Author(s) See Also Examples

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.

This package was not yet installed at build time.
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: This package was not yet installed at build time.
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)