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Old 11-03-2011, 12:54 AM   #1
accipiter
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Default What is the header format for Interval List in PicardTools?

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
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Old 11-03-2011, 01:06 PM   #2
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bump.... Anyone?
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Old 11-03-2011, 05:10 PM   #3
lek2k
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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
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Old 11-04-2011, 12:00 AM   #4
LiLin
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such as:
chr1:726340-727101
chr1:121352000-121352614
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Old 11-04-2011, 12:30 AM   #5
accipiter
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Quote:
Originally Posted by lek2k View Post
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
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Old 04-17-2012, 02:37 PM   #6
manducasexta
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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.
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