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Write NIPTeR-style bin counts to a bgzipped BED file

nipter_bin_bam_bed.Rd

Bins a BAM/CRAM file with NIPTeR defaults and writes the result to a bgzipped, tabix-indexed BED file.

Usage

nipter_bin_bam_bed(
  bam,
  bed,
  binsize = 50000L,
  mapq = 0L,
  require_flags = 0L,
  exclude_flags = 0L,
  rmdup = c("none", "flag"),
  separate_strands = FALSE,
  corrected = NULL,
  con = NULL,
  reference = NULL,
  index = TRUE
)

Arguments

bam

Path to an indexed BAM or CRAM file.

bed

Path for the output .bed.gz file. The tabix index is written alongside as paste0(bed, ".tbi").

binsize

Bin size in base pairs (default 50000).

mapq

Minimum mapping quality (default 0L). Set to 40L to match common NIPT pre-filtering (samtools view --min-MQ 40).

require_flags

Integer bitmask; only reads with all bits set are kept (samtools -f). Default 0L.

exclude_flags

Integer bitmask; reads with any bit set are dropped (samtools -F). Default 0L. Set to 1024L to exclude duplicate-flagged reads (samtools view -F 1024).

rmdup

Duplicate removal strategy: "none" (default) or "flag".

separate_strands

Logical; when TRUE, includes separate count_fwd and count_rev columns for forward- and reverse-strand counts. Default FALSE.

corrected

Optional NIPTeRSample already processed by nipter_gc_correct(). When supplied, its corrected counts populate the corrected_count column; otherwise the column is NA.

con

Optional open DBI connection with duckhts already loaded.

reference

Optional FASTA reference path for CRAM inputs.

index

Logical; create a tabix index (default TRUE).

Value

bed (invisibly).

Details

When separate_strands = FALSE (default), the output has five columns: chrom, start, end, count, corrected_count.

When separate_strands = TRUE, the output has nine columns: chrom, start, end, count, count_fwd, count_rev, corrected_count, corrected_fwd, corrected_rev. count is the total (forward + reverse); corrected_count is the total of the per-strand corrected values.

corrected_count (and corrected_fwd/corrected_rev) is NA until a GC-corrected sample is supplied via the corrected parameter.

See also

nipter_bin_bam(), nipter_gc_correct(), bam_convert_bed()

Examples

if (FALSE) { # \dontrun{
nipter_bin_bam_bed("sample.bam", "sample.nipter.bed.gz")

# With pre-filtering matching a typical NIPT pipeline
nipter_bin_bam_bed("sample.dm.bam", "sample.nipter.bed.gz",
                   mapq = 40L, exclude_flags = 1024L)

# Strand-separated output (9 columns)
nipter_bin_bam_bed("sample.bam", "sample.stranded.bed.gz",
                   separate_strands = TRUE)
} # }