Get read positions from BAM-file

Source: R/get_read_positions_from_BAM_indels.R

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

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.