README

# Works for human and mouse
# somatic mutation calling with matched normal sample is very stingent
# germline mutation calling and somatic mutation calling without matched normal is loose

somatic.pl: pipeline for somatic and germline mutation calling				for each sample		
job_somatic.pl: biohpc submission wrapper for somatic.pl				for a batch of samples	
filter.R: post-processing script for somatic mutations					for a batch of samples	

cnv.pl: pipeline for somatic CNV calling and quality check				for each sample		
job_cnv.pl: biohpc submission wrapper for cnv.pl					for a batch of samples	
summarize_cnv.R: summarizing script for CNV and quality check callings			for a batch of samples	

evolution.pl: inferring evolutionary relationships using mutation and CNV results 	for a batch of samples from one patient

Updates:

12/13/2018: Enabled mouse mutation and cnv calling
01/09/2019: Included COSMIC consensus gene annotation in the mutation summary tables
01/28/2019: Fixed the protein sequence annotation issue 
03/31/2019: Added the evolution.pl script
04/05/2019: Added the $debug hidden parameter
04/15/2019: Added handling of single end sequencing data