FFPEReadFilter: Find and filter artifact chimeric reads in BAM file of FFPE...
In LanyingWei/FilterFFPE: FFPE Artificial Chimeric Read Filter for NGS data

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/Main.R

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.

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)

`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. For paired-end sequencing, a read pair of artifact chimeric fragments may both contain the artifact breakpoints; thereby, the defalut is set to 2.
`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 regions (SRCR). Reads with SRCR shorter than this length are not recognized as artifact chimeric reads. Note: sequence errors and mutations might influence the detection of the existence and length of SRCR. Suggested range: 0-3. When it is set to 0 or any value below 1, this step will be skipped.
`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.

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.

The file name of the created destination file.

Lanying Wei <lanying.wei@uni-muenster.de>

FilterFFPE, findArtifactChimericReads, filterBamByReadNames

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)