filterBamByReadNames: Filter reads from BAM file by read names

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

Description

Generate filtered BAM file that does not contain reads with the input read names.

Usage

filterBamByReadNames(file, readsToFilter, index=file,
destination=sub("\\.bam(\\.gz)?", ".FilterFFPE.bam", file), overwrite=FALSE)

Arguments

file	Path to the input BAM file.
readsToFilter	A character vector of read names to filter.
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.

Details

Generate filtered BAM file that does not contain reads with the input read names, index file is also created.

Value

The file name of the created destination file.

Author(s)

Lanying Wei <[e-mail]>

See Also

FilterFFPE, findArtifactChimericReads, FFPEReadFilter

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")
artifactReads <- findArtifactChimericReads(file = file, threads = 2,
                                           FFPEReadsFile = FFPEReadsFile,
                                           dupChimFile = dupChimFile)
dupChim <- readLines(dupChimFile)
readsToFilter <- c(artifactReads, dupChim)
filterBamByReadNames(file = file, readsToFilter = readsToFilter,
                     destination = destination, overwrite=TRUE)

LanyingWei/FilterFFPE documentation built on Nov. 13, 2020, 3:58 a.m.