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        "author": "Brent Pedersen",
        "author_email": "bpederse@gmail.com",
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            "License :: OSI Approved :: MIT License",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "mendelian-error\n===============\n\nThis package attempts to assign probability to a mendelian error event in a trio.\nFor example, given a mother with genotype 'C/C' and a father with genotype 'C/C'\na child with genotype 'C/T' will be a \"mendelian error\", in this case, a candidate\n*de novo* mutation.\n\nWe can filter candidates based on their genotype likelihoods. For example if the\nchild had a genotype likelihood of -2,-1,-20 then we are likely to consider this\na genotyping error because the homozygous reference (\"C/C\" with GL -2) is fairly\nclose the the GL for het (with GL -1). If the genotype likelihood field was\n-20,0,-20, then the call is confidently het. We can use the genotype likelihoods\nto assign a probability:\n\n```Python\n\n>>> from mendelianerror import mendelian_error\n# everyone is homref. this should have a low probability of an error:\n>>> father = mother = child = [-0.1, -8.0, -8.0]\n>>> mendelian_error(mother, father, child)\n7.55...e-08\n\n\n# parents are hom, child is het. this is a likely mendelian error:\n>>> father = mother = [-0.6, -2.5, -2.5]\n>>> child = [-2.5, -0.6, -2.5]\n>>> mendelian_error(mother, father, child)\n0.987...\n\n```\n\nSo the input is the 3 GL numbers for each of the father, mother, child.\n\nInstallation\n============\n\n    pip install mendelianerror\n\nCLI\n===\n\nAfter installation, one can use this on a multi-sample VCF file like:\n```Shell\nmendelianerror $input.vcf father_id mother_id child_id > $new.vcf\n```\n\nto get only the putative mendelian errors, set a high cutoff:\n\n```Shell\nmendelianerror --cutoff 0.999 $input.vcf father_id mother_id child_id > $new.vcf\n```\n\n\nLimitations\n===========\n\n+ Only make sense for autosomal variants.\n+ Only works on trios (doesn't consider extended pedigrees or siblings).",
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