get_read_positions_from_BAM_indels: Get read positions from BAM-file

In JakobPedersenLab/dreams: Deep Read-level Error Model for Sequencing data

Get read positions from BAM-file

Description

This functions extracts information about read position that cover positions of interest in a BAM-file.

Usage

get_read_positions_from_BAM_indels(
  bam_file_path,
  chr,
  genomic_pos,
  reference_path,
  batch_size = NULL
)

Arguments

bam_file_path	Path to BAM-file.
chr, genomic_pos	Vectors. Should specify the positions of interest (chr = Chromosome, genomic_pos = Position in chromosome)
reference_path	Path to reference genome e.g. FASTA-file.
batch_size	Number of positions to process at a time

Value

data.frame(). Each line describes a position in a read.

JakobPedersenLab/dreams documentation built on Feb. 2, 2024, 3:14 p.m.