#picard tools to get some insert statistics to see whether our reads seem to be in the correct place
#module load picard/2.0.1
java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/picard.jar CollectInsertSizeMetrics MINIMUM_PCT=0 HISTOGRAM_FILE=<assembly name>.pdf INPUT=<sorted-bam-filename> OUTPUT=<assembly name>.sorted.collectInseSize HISTOGRAM_WIDTH=500
