subSampleBam: Subsample a bam file according to coverage

In DKMS-LSL/dr2s: Dual redundant reference sequencing

Description

Subsample a bam file according to coverage

Usage

subSampleBam(
  bamfile,
  windowSize = NULL,
  sampleSize = 100,
  fragmentReads = FALSE,
  fragmentWidth = 1000,
  what = NULL,
  clusteredReads = NULL,
  paired = FALSE
)

Arguments

bamfile	The bamfile that will be subsampled
windowSize	The window size for subsampling. The number of reads precised by sampleSize argument will be sampled in this window.
sampleSize	The desired new coverage of the bamfile.
what	What to extract from the bam file to write to the new one. If NULL defaults to the complete output of scanBamWhat.

Value

A list containing the filename of the original bamfile, the name of the new bamfile, the reference length and the sampleSize

DKMS-LSL/dr2s documentation built on March 14, 2021, 2:46 p.m.