filteroutBam: Filter bam
In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

filteroutBam

R Documentation

Filter bam

Description

Filter bam file by removing...

Usage

  filteroutBam(inBam, outBam, cores = ezThreads(), chrs = NA)

Arguments

`inBam`	`character`(1): the input bam file.
`outBam`	`character`(1): the output bam file.
`cores`	`integer`(1): the number of threads to use.
`chrs`	`character`(n): the chromosomes to filter out.
`mapQ`	`integer`(1): The minimal mapping quality for alignments.

Value

invisible outBam file

Author(s)

Ge Tan

Examples

  inBam <- system.file("extdata", "ex1.bam", package="Rsamtools", 
                       mustWork=TRUE)
  outBam <- tempfile(pattern="test-", fileext=".bam")
  filteroutBam(inBam, outBam, chrs="seq1", mapQ=10)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.