bam2R: Read nucleotide counts from a .bam file

In gerstung-lab/deepSNV: Detection of subclonal SNVs in deep sequencing data.

Read nucleotide counts from a .bam file

Description

This function uses a C interface to read the nucleotide counts on each position of a .bam alignment. The counts of both strands are reported separately and nucleotides below a quality cutoff are masked. It is called by deepSNV to parse the alignments of the test and control experiments, respectively.

Usage

bam2R(
  file,
  chr,
  start,
  stop,
  q = 25,
  mq = 0,
  s = 2,
  head.clip = 0,
  max.depth = 1e+06,
  verbose = FALSE,
  mask = 0,
  keepflag = 0,
  max.mismatches = NULL
)

Arguments

file	The name of the .bam file as a string.
chr	The chromosome as a string.
start	The start position (1-indexed).
stop	The end position (1-indexed).
q	An optional cutoff for the nucleotide Phred quality. Default q = 25. Nucleotides with Q < q will be masked by 'N'.
mq	An optional cutoff for the read mapping quality. Default mq = 0 (no filter). reads with MQ < mq will be discarded.
s	Optional choice of the strand. Defaults to s = 2 (both).
head.clip	Should n nucleotides from the head of reads be clipped? Default 0.
max.depth	The maximal depth for the pileup command. Default 1,000,000.
verbose	Boolean. Set to TRUE if you want to get additional output.
mask	Integer indicating which flags to filter. Default 0 (no mask). Try 3844 (UNMAP|SECONDARY|QCFAIL|DUP|SUPPLEMENTARY).
keepflag	Integer indicating which flags to keep. Default 0 (no mask). Try 3 (PAIRED|PROPERLY_PAIRED).
max.mismatches	Integer indicating maximum NM value to allow in a read. Default NULL (no filter).

Value

A named matrix with rows corresponding to genomic positions and columns for the nucleotide counts (A, T, C, G, -), masked nucleotides (N), (INS)ertions, (DEL)etions, (HEAD)s and (TAIL)s that count how often a read begins and ends at the given position, respectively, and the sum of alignment (QUAL)ities, which can be indicative of alignment problems. Counts from matches on the reference strand (s=0) are uppercase, counts on the complement (s=1) are lowercase. The returned matrix has 11 * 2 (strands) = 22 columns and (stop - start + 1) rows.

Author(s)

Moritz Gerstung

Examples

## Simple example:
counts <- bam2R(file = system.file("extdata", "test.bam", package="deepSNV"), chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 3120, stop=3140, q = 10, mask = 3844)
show(counts)
## Not run: Requires an internet connection, but try yourself.
# bam <- bam2R(file = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam", chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 2074, stop=3585, q=10, mask = 3844)
# head(bam)

gerstung-lab/deepSNV documentation built on June 3, 2022, 3:05 p.m.