downsampleBam: Randomly downsample bam file to a target depth

In hw538/cfDNAPro: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

Randomly downsample bam file to a target depth

Description

Randomly downsample bam file to a target depth

Usage

downsampleBam(
  bamfile,
  genome = NA_character_,
  input_depth = NULL,
  input_mapped_reads_count = NULL,
  output_depth = 0.1,
  output_type = c("bam", "rds"),
  output_dir = NULL,
  return_result = TRUE,
  ...
)

Arguments

bamfile	String. A bam file.
genome	Single String or NA. Supported values: "hg19", "hg38", or "GRCh38". Used for setting the seqinfo in the resulting GALP object.
input_depth	Numerical. If not supplied, infer the depth based on the total mapped paired reads in the input bam file.
input_mapped_reads_count	Numerical. If not supplied, infer the depth based on the total mapped reads in the input bam file.
output_depth	Numerical. Default is 0.1, which mean 0.1x target depth after downsampling.
output_type	Vector. Default is c("bam", "rds"), which means saving the downsampled bam as bam file AND rds file (i.e. GAlignmentPairs object).
output_dir	String. If not supplied, it will be set as the same folder with input bamfile.
return_result	Boolean. TRUE(default) means the result will be returned as an R object to console or the designated object.
...	further parameters for bam_to_galp2 function.

Value

GAlignmentPairs object containg the downsampled reads.

hw538/cfDNAPro documentation built on April 21, 2024, 2:21 a.m.