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Old 03-07-2012, 12:30 AM   #1
pravee1216
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Default Estimate on-target coverage for exome data

Hello,

I was looking for a one-stop tool which takes BAM and target capture regions to provide a detailed summary with coverage estimates on-target/off-target regions for exome-seq, but I didn't see any such as of now. (There are tools that generate coverage files such as GATK's depth_of_coverage, BEDtools, but none of them provide *summary* of on/off-target bases/%)

Does anyone have any experience / know any such tools?

Raj
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Old 03-07-2012, 01:06 AM   #2
Bukowski
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You could use Picard "CollectMultipleMetrics" and "HSMetrics" which tends to cover most things people want to know
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Old 03-07-2012, 10:18 AM   #3
pravee1216
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Thanks for the quick reply. I have seen these tools, but "HsMetrics" require a bait file in addition to the target .bed. I have the target file, but I have no idea how to get the bait file and moreover its importance here, as target .bed can estimate the required matrics?

Do you have any idea how to generate/download the bait file for particular exon capture experiment or is this provided by Agilent/Nimblegen?

Best,

Raj
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Old 03-07-2012, 10:40 AM   #4
Heisman
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Quote:
Originally Posted by pravee1216 View Post
Thanks for the quick reply. I have seen these tools, but "HsMetrics" require a bait file in addition to the target .bed. I have the target file, but I have no idea how to get the bait file and moreover its importance here, as target .bed can estimate the required matrics?

Do you have any idea how to generate/download the bait file for particular exon capture experiment or is this provided by Agilent/Nimblegen?

Best,

Raj
I use the same file for baits and targets.
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Old 03-07-2012, 10:42 PM   #5
dnusol
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You could also try NGSrich

http://sourceforge.net/projects/ngsrich/
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Old 03-08-2012, 12:39 AM   #6
Bukowski
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Quote:
Originally Posted by pravee1216 View Post
Thanks for the quick reply. I have seen these tools, but "HsMetrics" require a bait file in addition to the target .bed. I have the target file, but I have no idea how to get the bait file and moreover its importance here, as target .bed can estimate the required matrics?

Do you have any idea how to generate/download the bait file for particular exon capture experiment or is this provided by Agilent/Nimblegen?

Best,

Raj
As Heisman said you could just use the same file. I don't because I have separate baits and targets files (for SureSelect you can get these from e-Array), but in practice the on-bait and on-target figures don't differ that much that I would care about it..
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Old 03-08-2012, 03:27 AM   #7
pravee1216
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Thanks for the reply. I would try both NGSrich as well as Picard metrics. I hope NGSrich can summarize with coverage plots (as explained here http://seqanswers.com/forums/archive...p/t-10014.html)
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Old 03-18-2012, 09:15 AM   #8
pravee1216
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NGSrich is really good, but the number of reads (i.e., # reads) output is quite confusing as it gives a very low count, compared to the original total reads/on-target. For eg: # of reads say 0.2 million out of 150 million total reads, which is wrong. Have you ever noticed this before (in version 0.7.6)?
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Old 03-19-2012, 08:32 AM   #9
dnusol
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No, I have not noticed that problem using v0.7.5
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Old 04-12-2012, 06:14 AM   #10
annblack
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Default NGSRich target reads low

Hi - I noticed the same thing and opened a bug w/ the developer. He has fixed the read length issue and posted a new version of the tool.

Thanks!
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Old 04-12-2012, 11:20 AM   #11
swbarnes2
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A pretty simple way...count how many reads align to the whole genome, use BEDtools to filter the whole .bam with a .bed file of your targets. Then count how many reads are in the filtered .bed file.
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