How To Make Bait_Intervals In Picard

Question

[User 1933]

Basically what is the difference of BAIT_INTERVALS and TARGET_INTERVALS and secondly, How BAIT_INTERVALS, should be generated ?

Answer 1

[Jorge Amigo]

the definition of both parameters is very clear on the CalculateHsMetrics tool. a little bit more explained would be as follows:

• when you have a region or a set of regions of interest you can define them on a "chr start stop" format bed file. this would be your target region, and it is what Picard expects to be the TARGET_INTERVALS file. this is what you WANT to sequence.
• when you go with your target to the enrichment design tool, you are requiring baits that cover your regions. those baits should always overlap your target region, but there could be cases where you can't have baits to cover your target, or they may cover additional bases outsite of your target. if those regions covered by the designed baits are stored into a bed file, it is what Picard expects to be the BAIT_INTERVALS file. this is what you are REALLY going to sequence.

since both files can be different, Picard allows to generate statistics though CalculateHsMetrics for both files, providing stats on both the regions that you were interested in and the regions that you really sequenced. since most of the times we users end up handling the target region bed file only, and Picard complains if any of these parameters isn't defined, it is a common practice to use that same bed file to fill both the TARGET_INTERVALS and the BAIT_INTERVALS parameters, ending up logically with the same stats duplicated in the output file.