filtOutBAM: Filter out reads from BAM file

In mireia-bioinfo/pipelineNGS: Methods for Epigenetic Data Processing

Filter out reads from BAM file

Description

Function that filters out the following reads: 1) aligned no non-cannonical chromosomes, 2) not aligned, 3) aligned to ENCODE blacklisted regions and 3) duplicated reads.

Usage

filtOutBAM(
  file,
  path_logs,
  type = "SE",
  remove = c("chrM", "chrUn", "_random", "_hap", "_gl", "EBV"),
  blacklist = "~/data/consensusBlacklist.bed",
  cores = 6
)

Arguments

file	Filenme and path for the BAM file to be filtered out.
path_logs	Character indicating the output directory for the logs.
type	Sequence type, one of "SE" (single end) or "PE" (paired end).
remove	Character vector with chr that will be filtered out. Any chromosome name containing matches for these characters will be removed.
blacklist	Character indicating the file containing blacklist regions in bed format. Any reads overlapping these regions will be discarded.
cores	Number of cores to use for the analysis.

Value

File without the ".raw" preffix containing the final reads, along with its index (.bai). Also returns invisibly the name of the output file.

Examples

## Not run: 
file <- filtOutBAM(file=file,
                   path_logs=path_logs,
                   cores=8)

## End(Not run)

mireia-bioinfo/pipelineNGS documentation built on Jan. 2, 2023, 11:18 a.m.