splitBAM: Split a bam file by given criteria
In vivekbhr/vivlib: An R package for useful bioinformatics wrappers

Description Usage Arguments Value Examples

Split a bam file by given criteria

1 2	splitBAM(bamFile, splitby = "strand", chrnameList = NULL, flagList = NULL, mapqList = NULL, outfile_prefix, nthreads = 20)

`bamFile`	Bam file path
`splitby`	How to split the file ("strand","chr","flag","mapq")
`chrnameList`	list of Chromosomes to split by
`flagList`	List of samflags to split by
`mapqList`	List of mapq cutoffs to split by (reads with mapq greater than cutoff will be kept)
`outfile_prefix`	prefix for output filename
`nthreads`	Number of threads to use

Splitted, sorted and indexed bam files

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bam <- system.file("extdata", "test_2L2R.bam", package="vivlib")
splitBAM(bam = bam, splitby = "chr", chrnameList = NULL, flagList = NULL,
             mapqList = NULL, outfile_prefix = "test", nthreads = 20)