What is the header format for Interval List in PicardTools?

[accipiter]

Hi,

I have aligned paired-end read data from from a gene resequencing project, and am attempting to run the CalculateHsMetrics tool from PicardTools suite to calculate various metrics, and have a question re interval lists.

In order to derive % on-target, I need to define locations of baits, and target intervals. This is not a problem, but I cant figure out what the header should look like. The main reference often referred to re formatting of the interval list header is this: http://picard.sourceforge.net/javado...ervalList.html

... but I was looking for an actual example, and/or how to generate a header that will work with my processed bam file.

Thanks in advance,

Dave

[accipiter]

bump.... Anyone?

[lek2k]

There is an example on the GATK website
http://www.broadinstitute.org/gsa/wi...line_arguments

Here's a direct link to the file if you don't wanna read all the text
ftp://ftp.broadinstitute.org/pub/gsa....interval_list

[LiLin]

such as:
chr1:726340-727101
chr1:121352000-121352614

[accipiter]

There is an example on the GATK website
http://www.broadinstitute.org/gsa/wi...line_arguments

Here's a direct link to the file if you don't wanna read all the text
ftp://ftp.broadinstitute.org/pub/gsa....interval_list

Thanks, I'm assuming that the header is specific to my reference genome.
Probably a basic question, but how do I go about generating it so that it matches the contig locations in my reference genome specifically?

thanks

[manducasexta]

For the possible benefit of future searchers: I found the properly formatted header in the .dict file corresponding to the genome I am using. The .dict file was generated by GATK and can be generated in isolation as described at this link referred to above.