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  • GATK 'Variant quality score recalibration' for shallow coverage

    Hello,

    I've used GATK to produce variant calls (VCF files). I have shallow coverage (<10) and the documentation suggests using 'Variant quality score recalibration' according to 'true sites' from HapMap 3 and Omni 2.5M SNP chip array. My question is, will I loose all the variants not occuring on those controls? For example, will I loose novel variant?

    any advise on this is welcome

    Thanks
    Jorge

  • #2
    Hello,

    those sets with "true sites" are used to build an error model then each snp will be given a score based on the error model and the other parameters that has been collected.

    So you will not loose any information.

    Comment


    • #3
      Hello!

      Thanks a lot for clarifying that!

      Jorge

      Comment

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