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- 8 months ago
Posts by minma
... I'm trying to identify polymorphisms in three samples. I'm usng Varscan and the default p-value threshold for calling variants is 0.99. If I want to get a false discovery call of 1/10.000 or better, should I set the p-value threshold as 0.00001? Deffault values seem too high... am I wrong? ...
... I'm trying to identify polymorphisms in three samples. When I get the VCF file there are many variants with with the NC value higher than 0. Should I remove these variants from the VCF file? ...
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