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Old 04-08-2011, 04:28 AM   #1
Seq84
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Location: Italy

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Default Coverage assessment

Hi,

We are making a target resequencing experiment in 6 differents regions. During coverage assessment with DepthOfCoverage walker in GATK we noticed that regions rich in GC (high %GC) were characterize by lower coverage values compare to ones in low-normal %GC regions.

How the % in GC can affect coverage in a target resequencing experiment?

Thanks in advance
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Old 04-18-2011, 02:37 PM   #2
visivas
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We found similar distribution of coverage for targeted resequencing experiment with %GC compared to whole genome. We had peak coverage in regions that had between 30%-70% GC content.
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