Is it possible to get same SNVs in all the samples? Or is it false positives?

jagritijagriti indiaPosts: 2Member

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

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,428Administrator, GATK Developer admin

    Hi Jagriti,

    It is difficult to say without seeing the calls. Generally speaking, if you are looking at an entire human genome, it is expected that your samples will have many SNVs in common. If you have followed the Best Practices recommendations (including variant filtering or recalibration) then you have a good chance that your results are okay. But it is up to you to evaluate your callset.

    Geraldine Van der Auwera, PhD

  • jagritijagriti indiaPosts: 2Member

    One thing I forgot to mention is that we are analyzing whole exome sequencing data. 1% of SNVs has come out to be common in all samples. pleasae help out!

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,428Administrator, GATK Developer admin

    I'm sorry but I can't help you unless you have a specific problem with our tools. Analyzing and understanding your results is your job...

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.