Metadata-Version: 1.1
Name: mendelianerror
Version: 0.0.1
Summary: probability of mendelian error in trios
Home-page: UNKNOWN
Author: Brent Pedersen
Author-email: bpederse@gmail.com
License: UNKNOWN
Description: mendelian-error
        ===============
        
        This package attempts to assign probability to a mendelian error event in a trio.
        For example, given a mother with genotype 'C/C' and a father with genotype 'C/C'
        a child with genotype 'C/T' will be a "mendelian error", in this case, a candidate
        *de novo* mutation.
        
        We can filter candidates based on their genotype likelihoods. For example if the
        child had a genotype likelihood of -2,-1,-20 then we are likely to consider this
        a genotyping error because the homozygous reference ("C/C" with GL -2) is fairly
        close the the GL for het (with GL -1). If the genotype likelihood field was
        -20,0,-20, then the call is confidently het. We can use the genotype likelihoods
        to assign a probability:
        
        ```Python
        
        >>> from mendelianerror import
        # everyone is homref. this should have a low probability of an error:
        >>> father = mother = child = [-0.1, -8.0, -8.0]
        >>> mendelian_error(mother, father, child)
        7.55...e-08
        
        
        # parents are hom, child is het. this is a likely mendelian error:
        >>> father = mother = [-0.6, -2.5, -2.5]
        >>> child = [-2.5, -0.6, -2.5]
        >>> mendelian_error(mother, father, child)
        0.987...
        
        ```
        
        So the input is the 3 GL numbers for each of the father, mother, child.
        
        CLI
        ===
        
        After installation, one can use this on a multi-sample VCF file like:
        ```Shell
        mendelianerror $input.vcf father_id mother_id child_id > $new.vcf
        ```
        
        Limitations
        ===========
        
        + Only make sense for autosomal variants.
        + Only works on trios (doesn't consider extended pedigrees or siblings).
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
