pileupMT: Pileup the mitochondrial reads in a BAM, for variant calling...

In trichelab/MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis

Description

If a BAM filename is given, but no ScanBamParam, scanMT(bam) will be called. Human mitochondrial genomes (GRCh37+ and hg38+) are fully supported, mouse mitochondrial genomes (C57BL/6J aka NC_005089) are only somewhat supported.

Usage

pileupMT(
  bam,
  sbp = NULL,
  pup = NULL,
  callIndels = TRUE,
  ref = c("rCRS", "GRCh37", "GRCh38", "hg38", "GRCm38", "C57BL/6J", "NC_005089",
    "mm10"),
  ...
)

Arguments

bam	BAM (must be indexed!) file name or object with @bam slot
sbp	optional ScanBamParam object (autogenerated if missing)
pup	optional PileupParam object (autogenerated if missing)
callIndels	call indels? (This can reduce compute and RAM if FALSE.)
ref	aligned reference mitogenome (default is rCRS/GRCh37+)
...	additional args to pass on to the pileup() function

Value

       an MVRanges object, constructed from pileup results 

Examples

library(MTseekerData)
BAMdir <- system.file("extdata", "BAMs", package="MTseekerData")
patientBAMs <- list.files(BAMdir, pattern="^pt.*.bam$")
(bam <- file.path(BAMdir, patientBAMs[1]))
(sbp <- scanMT(bam))
(mvr <- pileupMT(bam, sbp=sbp, callIndels=TRUE, ref="rCRS"))

trichelab/MTseeker documentation built on March 8, 2021, 6:20 p.m.