bam2R: Read nucleotide counts from a .bam file
In deepSNV: Detection of subclonal SNVs in deep sequencing data.

Description Usage Arguments Value Author(s) Examples

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.

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
)

`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 1796 (BAM_DEF_MASK).
`keepflag`	Integer indicating which flags to keep. Default 0 (no mask). Try 3 (PAIRED\|PROPERLY_PAIRED).
`max.mismatches`	Integer indicating maximum MN value to allow in a read. Default NULL (no filter).

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.

Moritz Gerstung

## 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 = 1769)
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 = 1796)
# head(bam)