Is it possible to get same SNVs in all the samples? Or is it false positives?
Posted in Ask the GATK team | Last updated on


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Dear team, We have been analyzing caucasian samples of various origins against HG19, and we obtained various SNVs which are present in all the samples. Some of these mutations are relevant to the disease that we are studying. So we were wondering that whether it is possible to get such a result or are these false positives. These SNVs have Phred Quality score above 30. Can you tell whether data quality is bad if we get such a result. We are getting around 2000 such SNVs and our average coverage is 15X.

Thanks. Sincerely, Jagriti


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