FFPEReadFilter: Find and filter artifact chimeric reads in BAM file of FFPE...

In FilterFFPE: FFPE Artificial Chimeric Read Filter for NGS data

Description

Artifact chimeric reads are enriched in NGS data of FFPE samples, these reads can lead to a large number of false positive SV calls. This function finds and filters these artifact chimeric reads.

Usage

FFPEReadFilter(file, maxReadsOfSameBreak=2, minMapBase=1, threads=1,
index=file, destination=sub("\\.bam(\\.gz)?", ".FilterFFPE.bam", file),
overwrite=FALSE, FFPEReadsFile=sub("\\.bam(\\.gz)?", ".FFPEReads.txt", file),
dupChimFile=sub("\\.bam(\\.gz)?", ".dupChim.txt", file), filterdupChim=TRUE)

Arguments

file	Path to the BAM file.
maxReadsOfSameBreak	The maximum allowed number of artifact chimeric reads sharing a false positive breakpoint. If the number of reads sharing the same breakpoint exceeds this number, these reads are not recognized as artifact chimeric reads. Reads marked as PCR or optical duplicates are excluded from the calculation.
minMapBase	The minimum required length (bp) of a short complementary mapping for an artifact chimeric read. Artifact chimeric reads are derived from the combination of two single-stranded DNA fragments linked by short reverse complementary mapping. Reads with such complementary sequences shorter than this length are not recognized as artifact chimeric reads.
threads	Number of threads to use. Multi-threading can speed up the process.
index	Path of the index file of the input BAM file.
destination	Path of the output filtered BAM file.
overwrite	Boolean value indicating whether the destination can be over-written if it already exists.
FFPEReadsFile	Path of the output txt file with artifact chimeric read names.
dupChimFile	Path of the output txt file with supplementary reads that are marked as PCR or optical duplicates.
filterdupChim	Filter PCR or optical duplicates of all chimeric reads. when set to true. These reads may contain duplicates of artifact chimeric reads; therefore, it is recommended to also remove these reads.

Details

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 function finds and filters these artifact chimeric reads. An index file is also generated for the created filtered BAM file.

Value

The file name of the created destination file.

Author(s)

Lanying Wei <[e-mail]>

See Also

FilterFFPE, findArtifactChimericReads, filterBamByReadNames

Examples

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)

FilterFFPE documentation built on Nov. 8, 2020, 8:10 p.m.