Generate some alignment statistics on reads

Generate some alignment statistics on reads

qc_alignment(samtools = "samtools", bam.files = NULL,
  filtered.bam.files = NULL, threads = 1,
  remove.mitochondrial = "MT")

Arguments

samtools	character string specifying path to samtools. [DEFAULT = "samtools"]
bam.files	character vector specifying path to pre-filtered bam files. [DEFAULT = NULL]
filtered.bam.files	character vector specifying path to filtered bam files. [DEFAULT = NULL]
threads	positive integer specifying the number of cores to use
remove.mitochondrial	character string. If set, this will count reads mapping to the mitochondrial genome. The string should match the reference name for the mitochondrial genome in the alignment file. Examples include "ChrM", "M" and "MT".