Hi,

I'm trying to run Picard's CollectTargetedPcrMetrics to get some metrics for my truseq amplicon assay. I'm unclear the difference between "AMPLICON_INTERVALS" vs "TARGET_INTERVALS". I think my question is I need a clear understanding of "baits" vs "targets". I google but didn't find a lot but my understanding is the "baits" is the "amplicon" primer with start, end position that used in the BED file and the amplicon_interval_list can be generated from the BedToIntervalList from Picard. But what I'm unclear is how to define "target" and how to generate the list?

Thanks!

definition from Picard: AMPLICON_INTERVALS (File) An interval list file that contains the locations of the baits used. Required. TARGET_INTERVALS (File) An interval list file that contains the locations of the targets. Default value: null. This option must be specified at least 1 times.

java -jar picard.jar CollectTargetedPcrMetrics \ I=input.bam \ O=pcr_metrics.txt \ R=reference_sequence.fasta \ AMPLICON_INTERVALS=amplicon.interval_list \ TARGET_INTERVALS=targets.interval_list