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Old 04-09-2013, 10:01 AM   #1
lewewoo
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Join Date: Apr 2011
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Default SNP filtering

I had a list of interesting SNPs from tumor samples, I am wondering how I can remove the SNP associated with population identified through HapMap or 1000 Genomes. I would like to pick one of the following two ways:
1) filter dbSNP131 and 1000 Genome using annovar;
2) filter dbSNP or 1000 Genome SNPs using BedTools to filter UCSC dbSNP 137.
After filtering, almost nothing left, the left SNPs should be high-confidence, right?
Thanks!
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