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  • Concrodance NGS and array genotypes

    Hi SEQanswers folks,

    for Sample based QC we would like to calculate the concordance of NGS genotypes from a VCF file and Illumina Array genotypes (HumanCoreExome-12 v1.0 ) from the FinalReport file.

    The VCF file consist the genotypes 1/1 or 0/1 whereas the FinalReport file has the genotypes in form of the alleles strand dependend.

    Extracted Infos from the VCF file

    chr start snp ref alt GT
    1 762273 rs3115849 G A 0 /1
    1 876499 rs4372192 A G 1/ 1
    1 877715 rs6605066 C G 1/ 1
    1 877831 rs6672356 T C 1 /1
    1 880238 rs3748592 A G 1 /1

    Extracted Infos from the FinalReport

    chr start marker allele A allele B

    1 152537954 exm-rs10888501 A G
    1 58915024 exm-rs10889092 G G
    1 63118196 exm-rs10889353 A C

    1 88112646 exm-rs10873862 A C
    1 76772328 exm-rs10873876 A G
    1 103133909 exm-rs10874639 A G
    1 93323971 exm-rs10874746 A A

    These are the infos I would use to estimate the concordance between the NGS and Array genotypes. Does someone have a clue how to approach this? Appreciate any help! Thx!
    Last edited by genomixer; 10-15-2015, 07:39 AM.

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