jvollme

#
# This script calculates the depth of coverage and breadth of coverage for a given bam. 
# Outputs a dictionary containing the contig/chromosome names and the depth and breadth of coverage for each
# and for the entire genome.
#
# If you optionally specify the name of the mitochondrial chromosome (e.g. mtDNA, chrM, chrMT)
# The script will also generate breadth and depth of coverage for the nuclear genome AND the ratio
# of mtDNA:nuclearDNA; which can act as a proxy in some cases for mitochondrial count within an individual.
# 
# Author: Daniel E. Cook