filter_fragments: Filter DNA fragments in BAM files by length and position
In TearsWillFall/DNAfrags: Filter DNA fragments in BAM files by length and location

View source: R/filter_fragments.R

filter_fragments

R Documentation

Filter DNA fragments in BAM files by length and position

Description

This function takes a BAM file as input and returns a filtered BAM file by size or/and position, or viceversa.

Usage

filter_fragments(
  bin_path = "tools/samtools/samtools",
  file = "",
  bed = "",
  min_frag_size = 0,
  max_frag_size = 1e+09,
  chr = "",
  start_pos = 1,
  end_pos = "",
  verbose = FALSE
)

Arguments

`bin_path`	Path to fastQC executable. Default path tools/samtools/samtools.
`file`	Path to the input file.
`bed`	Path to a BED input file with multiple genome positions. Default None
`min_frag_size`	Minimum fragment size to keep. Default 1.
`max_frag_size`	Maximum fragment size to keep. Default 100000000.
`chr`	Chromosome to keep. Only single chromosomes. Default None.
`start_pos`	Starting position to search within a chromosome. Default 1
`end_pos`	Last position to search within a chromosome. Default None
`verbose`	Enables progress messages. Default False.