Read BAM Files — bb_read_bam • bambamR

Reads BAM files using Rsamtools (if available) or the system samtools command as fallback.

Usage

bb_read_bam(
  path,
  index = TRUE,
  what = c("qname", "flag", "rname", "pos", "mapq", "cigar")
)

Arguments

path: Character. Path to a BAM file.
index: Logical. Whether to use/create a BAM index. Default TRUE.
what: Character vector. Fields to extract. Default includes basic alignment fields.

Value

A data.frame with alignment information including columns: qname, flag, rname, pos, mapq, cigar.

Examples

# \donttest{
# Requires a BAM file
# bam_df <- bb_read_bam("aligned.bam")
# }