Changes between Version 1 and Version 2 of MendelianQcPipelineIdea


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Timestamp:
Sep 26, 2010 9:42:38 PM (11 years ago)
Author:
yurii
Comment:

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  • MendelianQcPipelineIdea

    v1 v2  
    1717In classical Mendelian checks, it is not possible to tell, what person is more likely to be erroneously typed, and genotypes of all pedigree members are set to missing. With sequencing data, because coverage and quality info is available, it is natural an possible to estimate the chances that a particular person's genotype is likely to be wrong, and set this particular genotype to missing.
    1818
    19 These considerations bring the idea that Mendelian checks can further be incorporated into the TrioAwareVariantDiscoveryPipeline by addressing the questions like:
     19These considerations bring the idea that Mendelian checks can further be incorporated into the TrioAwarePhasingPipeline, DeNovoVariationPipeline, and TrioAwareVariantDiscoveryPipeline by addressing the questions like:
    2020* when one of parental genotypes is missing, could we infer his or her genotype? Clearly, if a child is AB, an one of the parents is AA and other is missing, this other parent should carry 'B' allele
    2121* for some 'Mendelian impossible' configurations, e.g. if both parents are AA, and the child is AB, given the depth and phasing info, could that be that actually one of the parents is AB