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Old 08-08-2012, 08:35 AM   #1
SeqVicious
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Location: New Hampshire

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Default How do calculate % of genome with >20x coverage?

Hi all,

I've searched through the forums for my question but I haven't found anything for my specific stat that I'm looking for. How do you figure out the % of your genome that had >20x coverage? I'm new to bioinformatics so scripting is not something I can do but I can run any program. Is there a program out there that can help me?

Thanks.

Last edited by SeqVicious; 08-08-2012 at 09:04 AM.
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Old 08-08-2012, 09:46 AM   #2
Bukowski
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Could use Picard HSmetrics:

http://picard.sourceforge.net/picard...html#HsMetrics

I know I use it for exome data, but feed it the right interval list and I'm sure it will work with whole genome. It will give you a column in the output:

PCT_TARGET_BASES_20X: The percentage of ALL target bases acheiving 20X or greater coverage.
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Old 08-08-2012, 10:13 AM   #3
aaronh
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GATK DepthOfCoverage will do this. http://www.broadinstitute.org/gsa/ga...ageWalker.html
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Old 08-08-2012, 10:47 AM   #4
SeqVicious
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Thank you. I am going to give GATK a try. Luckily I already have this installed.

Cheers.
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Old 08-08-2012, 09:48 PM   #5
Tong.W
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You can use SOAP2 or BWA for mapping the sequencing reads with the reference ,no matter DNA or RNA data .and then use SOAP.coverage to calculate the coverage and the depth.
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Old 08-09-2012, 03:56 AM   #6
stephwen
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You could also use the genomeCoverageBed command from the BEDTools suite.
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