I have some problems understanding the output of picards CollectHsMetrics. Because I don't have a bait file i uses my bed file with the target regions to produce the interval list.
java -jar picard.jar BedToIntervalList I=target.bed SD=genome.dict O=target.interval_list
This target interval list I now use for the BAIT parameter and the TARGET parameter:
java -jar picard.jar CollectHsMetrics I=Sample.bam O=hsmetrix.txt BI=target.interval_list TI=target.interval_list
In my understanding the results for ON_BAIT_BASES and ON_TARGET_BASES have to be the same as the interval list is the same (and also all other values where is differ between bait and target). But in my case I have this result:
Please help me understanding where this difference come from.
Thanks a lot.