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

Downsampling a BAM file to achieve a specified sequencing depth. Exports the data as a BAM file and/or an RDS file containing a 'GAlignmentPairs' object.

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	Path to a BAM file.
genome	Supported values: "hg19", "hg38", "GRCh38", or NA. Sets seqinfo.
input_depth	Target depth, inferred if not supplied.
input_mapped_reads_count	Mapped reads count to infer depth if not supplied.
output_depth	Target output depth after downsampling, default is 0.1.
output_type	Output file formats, default is c("bam", "rds").
output_dir	Directory for output files, defaults to input file directory.
return_result	If TRUE (default), returns result as an R object.
...	Additional parameters for 'bam_to_galp2' function.

Value

'GAlignmentPairs' object with the downsampled reads if return_result.

Examples

## Not run: 
  # Downsample a BAM file to 10% of its original depth
  result <- downsampleBam("/path/to/your.bam", genome = "hg38",
                          output_depth = 0.1, output_type = c("bam", "rds"),
                          return_result = TRUE)

## End(Not run)

hw538/cfDNAPro documentation built on Feb. 17, 2025, 6:09 p.m.