[GenoMax]

Part highlighted in red must be an incorrect addition to your command?

$ java -jar [COLOR="Red"]picard-tools-1.135[/COLOR]/media/C2F8EFBFF8EFAFB9/picard-tools-1.135/picard.jar CalculateHsMetrics BI=sam_sort_index_5column_xgen_probes.bed TI=sam_sort_index_5column_xgen_targets.bed I=IonXpress_009_150603_newheader.bam O=IonXpress_009_150603_all_IDT.CalculateHSmetrics

you could potentially just do

$ java -jar picard.jar CalculateHsMetrics BI=sam_sort_index_5column_xgen_probes.bed TI=sam_sort_index_5column_xgen_targets.bed I=IonXpress_009_150603_newheader.bam O=IonXpress_009_150603_all_IDT.CalculateHSmetrics

[cmccabe]

Thank you very much for all your help it getting this to work. I really appreciate it