https://bioinformaticsonline.com/snippets/view/42193/picard-tools-command-to-get-some-insert-statistics? https://bioinformaticsonline.com/snippets/view/42193/picard-tools-command-to-get-some-insert-statistics Sun, 06 Sep 2020 10:23:15 -0500 https://bioinformaticsonline.com/snippets/view/42193/picard-tools-command-to-get-some-insert-statistics #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]]> Neel