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Old 05-07-2012, 08:10 PM   #1
caswater
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Location: Canada

Join Date: Jun 2011
Posts: 47
Default snp call in Repeat Masked region

GATK gave me around 3.2 million SNPs, and I overlapped the SNPs with regions identified by repeatMasker, and found half are affected by RepeatMasker-defined repeats. I am just wondering if it is necessary to exclude the SNPs marked by repeat masker, or shall I just go with the SNPs passed the GATK filters? What's the common practice regarding this issue?

Thank you for your advice
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