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samples differ in coverage, how to set QUAL threshold in VariantFiltration

Hi :),
I'am new to NGS and have a questions reagarding the filtering.
I have 13 individuals, 3 of them with a coverage of 11x-15x, the rest with a coverage of 5x-7x. I did multi-sample SNPcalling and hard filtering, the latter as there are no known SNPs so far. Now I am not sure how to set the minimal SNP quality (QUAL). On the best practise it is suggested to juse at least 30 for individuals with a coverage of at least 30, but 4 if the coverage is below 10. So what is the best way to set the QUAL filter?

many thanks in advance

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    As answered in your other post, you are better off using the lower threshold for all of them for calling, but for filtering you need to be more stringent in order to eliminate false positives. Since your dataset is different from the "ideal" dataset that our Best Practices are based on, you will need to experiment a little to find the settings that work best for you.

  • hi geraldine, thanks again! How should i experiment? Extract one scaffold and look which SNPs will disappear/stay? or is this the wrong technique?
    Thanks for the great support of you and your tem!
    voalvi

  • Hi geraldine. I wanted to extract one scaffold to focus on a small region:) Many thanks for all the tips and help! Volavii

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