tallyBAM: tallyBAM
In h5vc: Managing alignment tallies using a hdf5 backend

Description Usage Arguments Details Value Author(s) Examples

Function for creating tallies from bam files.

1	tallyBAM(file, chr, start, stop, q=25, ncycles = 0, max.depth=1000000, verbose=FALSE, reference = NULL)

`file`	filename of the BAM file that should be tallies
`chr`	Chromosome in which to tally
`start`	First position of the tally
`stop`	Last position of the tally
`q`	quality cut-off for considering a base call
`ncycles`	number of sequencing cycles form the front and back of the read that should be considered unreliable
`max.depth`	only tally a position if there are less than this many reads overlapping it - can prevent long runtimes in unreliable regions
`verbose`	should additional information be printed
`reference`	`DNAString` object holding the reference sequence of the region being tallies, if this is `NULL` (the default) the raw tally is returned, otherwise `prepareForHDF5` is called with the raw tally and the reference and the prepared tally is returned instead

This function tallies nucleotides and deletion counts in the specified region of a given BAM file. The results can be processed with the prepareForHDF5 function.

This function was adapted from the bam2R function provided by the deepSNV package.

An array object with dimensions [stop - start + 1, 18, 2] which represent positions times nucleotides (4 bases + deletions + insertions times three for early, middle and late sequencing cycles) times strands.

Paul Pyl

library(h5vc)
files <- c("NRAS.AML.bam","NRAS.Control.bam")
bamFiles <- file.path( system.file("extdata", package = "h5vcData"), files)
chrom = "1"
startpos <- 115247090
endpos <- 115259515
theData <- lapply( bamFiles, function(bamf){
  tallyBAM( file = bamf, chr = chrom, start = startpos, stop = endpos, ncycles = 10 )
})
str(theData)
print(theData[[1]][,,,9491]) #position 9491 of the pileup