baseCountsFromBamList: Create a list object from a list of single-cell BAM files...

In veltenlab/mitoClone: Clonal tracking in single-cell RNA-seq data using mitochondrial and somatic mutations

Description

Uses the deepSNV package to count nucleotide frequencies at every position in the mitochondrial genome for every cell and passes the result to the mutationCallsFromDeepSNV function for filtering variants.

Usage

baseCountsFromBamList(bamfiles, sites = "chrM:1-16659", ncores = 20)

Arguments

bamfiles	A character vector specifying the bam file paths
sites	Vector specifying genomic regions, defaults to the entire mitochondrial genome.
ncores	Number of threads to use for the computation

Value

A list of base count matrices which can serve as an input to mutationCallsFromBlacklist or mutationCallsFromCohort

veltenlab/mitoClone documentation built on April 18, 2021, 5:19 a.m.