sortIndexBam: sortIndexBam

In ge11232002/NGS: Next Generation Sequencing Data Analysis

Description

sortIndexBam sort the bam file by coordinates and index it.

Usage

  sortIndexBam(inputs, outputs, maxMem="4096M", removeBam=TRUE,
               mc.cores=getThreads(), binary="samtools")

Arguments

inputs	The filenames of input bam files.
outputs	The filenames of output bam files.
maxMem	The maximal memory per thread to use.
removeBam	Remove the input bam files or not after sorting and idnexing.
mc.cores	The number of threads to use. By default, we use a internal function NGS:::getThreads to decide.
binary	The name/filename of the binary "samtools" to call.

Value

The output is returned.

Author(s)

Ge Tan

See Also

indexBam and sortBam, asBam from Rsamtools

Examples

  
  ## This example is not tested because it requires external software "samtools"
  library(Rsamtools)
  bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
                           mustWork=TRUE)
  sortIndexBam(inputs=bamfile, outputs="ex1_sorted.bam", removeBam=FALSE)
  

ge11232002/NGS documentation built on May 17, 2019, 12:13 a.m.