pileupVariants: Nucleotide pileup from alignments
In VariantTools: Tools for Exploratory Analysis of Variant Calls

Description Usage Arguments Value Author(s) See Also Examples

This is an alternative to tallyVariants for generating a VRanges from a set of alignments (BAM file) by counting the nucleotides at each position. This function uses the samtools-based applyPileups function, instead of bam_tally. Fewer dependencies, with fewer statistics (none beyond the fixed columns) available in the output.

1 2	pileupVariants(bams, genome, param = ApplyPileupsParam(), minAltDepth = 1L, baseOnly = TRUE, BPPARAM = defaultBPPARAM())

`bams`	A vector/list of BAM files as interpreted by `PileupFiles`.
`genome`	An object that provides sequence information via `getSeq`.
`param`	A `ApplyPileupsParam` object that specifies the mode of iteration and various filters.
`minAltDepth`	Minimal alt depth to be included in the output. The default avoids outputting results for positions/alleles that show no differences.
`baseOnly`	Whether to drop records with “N” in either the ref or alt.
`BPPARAM`	Not yet supported.

A VRanges object with read depth information for each position, allele, and sample.

Michael Lawrence

tallyVariants for more statistics.

bams <- LungCancerLines::LungCancerBamFiles()
if (requireNamespace("gmapR")) {
    param <- Rsamtools::ApplyPileupsParam(which=gmapR::TP53Which())
    pileup <- pileupVariants(bams, gmapR::TP53Genome(), param)
}