bam.cov.gr: Get coverage as GRanges from BAM on custom set of GRanges

In mskilab/bamUtils: Utility functions for manipulating BAMs

Get coverage as GRanges from BAM on custom set of GRanges

Description

Gets coverage from BAM in supplied GRanges using 'countBam()', returning GRanges with coverage counts in each of the provided GRanges (different from 'bamUtils::bam.cov()') specified as the columns $file, $records, and $nucleotides in the values field

Basically a wrapper for 'Rsamtools::countBam()' with some standard settings for 'Rsamtools::ScanBamParams()'

Usage

bam.cov.gr(
  bam,
  bai = NULL,
  intervals = NULL,
  all = FALSE,
  count.all = FALSE,
  isPaired = TRUE,
  isProperPair = TRUE,
  isUnmappedQuery = FALSE,
  hasUnmappedMate = FALSE,
  isNotPassingQualityControls = FALSE,
  isDuplicate = FALSE,
  mc.cores = 1,
  chunksize = 10,
  verbose = FALSE,
  ...
)

Arguments

bam	string Input BAM file. Advisable to make the input BAM a BamFile instance instead of a plain string, so that the index does not have to be reloaded.
bai	string Input BAM index file
intervals	GRanges of intervals to retrieve
all	boolean Flag to read in all of BAM as a GRanges via 'si2gr(seqinfo())' (default = FALSE)
isPaired	boolean Flag indicates whether unpaired (FALSE), paired (TRUE), or any (NA) read should be returned. See documentation for Rsamtools::scanBamFlag(). (default = NA)
isProperPair	boolean Flag indicates whether improperly paired (FALSE), properly paired (TRUE), or any (NA) read should be returned. A properly paired read is defined by the alignment algorithm and might, e.g., represent reads aligning to identical reference sequences and with a specified distance. See documentation for Rsamtools::scanBamFlag(). (default = NA)
isUnmappedQuery	boolean Flag indicates whether unmapped (TRUE), mapped (FALSE), or any (NA) read should be returned. See documentation for Rsamtools::scanBamFlag(). (default = NA)
hasUnmappedMate	boolean Flag indicates whether reads with mapped (FALSE), unmapped (TRUE), or any (NA) mate should be returned. See documentation for Rsamtools::scanBamFlag(). (default = NA)
isNotPassingQualityControls	boolean Flag indicates whether reads passing quality controls (FALSE), reads not passing quality controls (TRUE), or any (NA) read should be returned. See documentation for Rsamtools::scanBamFlag(). (default = FALSE)
isDuplicate	boolean Flag indicates that un-duplicated (FALSE), duplicated (TRUE), or any (NA) reads should be returned. 'Duplicated' reads may represent PCR or optical duplicates. See documentation for Rsamtools::scanBamFlag(). (default = FALSE)
mc.cores	integer Number of cores in mclapply (default = 1)
chunksize	integer How many intervals to process per core (default = 10)
verbose	boolean "verbose" flag (default = FALSE)
...	futher arguments passed into Rsamtools::scanBamFlag()

Value

GRanges parallel to input GRanges, but with metadata filled in.

mskilab/bamUtils documentation built on Sept. 28, 2022, 3:45 p.m.