Picard : Bait_interval and Target_interval

Question

[AIMAR]

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 for GATK is not really clear about it and I confused about what to do .

java -jar picard.jar BedToIntervalList
I=input.bed  #My Bed.file
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 ?

Thanks !

[Pierre Lindenbaum]

see bait interval list for picard collecthsmetrices ;

[GenoMax]

How do I get this file ?

You will have to get this file for the kit that was used for the project (is it an exome or something else). These are generally available from the kit manufacturers website. They may require you to create an account before you can access them.

[AIMAR]

Thanks for the response. I've a targeted panel of genes. But if I have the bed.file I can obtain the target and bait file by using picard BedToIntervals or I'm wrong ?

Also I've 2 bed.files one with more details (CHR | POSITION | Name of the region ) and the other one with just (CHR | POSITION ). I've decided to use the more detailed bed_file to generate the target_interval.file and the other one for the Bait_interval.file

And I'm asking if this is correct or something is wrong.

[GenoMax]

Are the intervals different in the two files or just that one file has the name (which is not essential for the tool). As noted in thread Pierre linked ( bait interval list for picard collecthsmetrices ) you can use one file for both (if you don't have two intervals in two files).

[AIMAR]

Yes the genomic position like for the first line are not the same.