Target_interval VS Bait_interval

[Aimar269]

Hello Picard Team, @yfarjoun
I was wondering if you got a chance to looks at this issue?
Thank you

Hi everyone, I'm actually working on a project and I'm using Picard for post-alignment processing.
I've a BED.file that describe the genomic regions targeted (CHROMOSOME | START POS | END POS | REGION_NAME ).

So I would like to know if using the same bed.file with Picad BedToIntervals for generating the Target_interval file and bait_interval file is normal or I have to use different file for each one ?
The documentation is not really clear about it and I confused about what to do .

java -jar picard.jar BedToIntervalList
I=input.bed
O=list.interval_list
SD=reference_sequence.dict

==============================
------------command--------------------------
java -jar picard.jar CollectHsMetrics
I=input.bam
O=hs_metrics.txt
R=reference_sequence.fasta
BAIT_INTERVALS=bait.interval_list \ #How do I get this file ?
TARGET_INTERVALS=target.interval_list ##How do I get this file ?

[kachulis]

Generally the bait intervals refer to the specific baits which are actually used to target the target regions. This would be something that the producer of the baits, or the sequencing data, might be able to provide you with.

If you can't get the baits used for your sequencing, you can just use the same file for both the BAIT_INTERVALS and TARGET_INTERVALS, with the caveat that you should then ignore any metrics which include the BAIT in them, and just use the TARGET metrics. You will be getting slightly less information about your data, but the difference will likely not be significant.