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  • Validation by genotyping arrays (SNP arrays) - why only heterozygous SNPs?

    Hi,

    I am trying to validate the variants I found using whole genome sequencing . The standard practice, I have seen in the two publications below were to check for the number of heterozygous SNPs called by the SNP array.

    1) Performance comparison of whole-genome sequencing platforms

    "To further assess the accuracy of the variant calling, ... Of the 260,112 heterozygous calls detected with the Omni array, 99.5% were present in the entire SNV data set, 99.34% were concordant calls and only 0.16% were platform-specific SNVs. This demonstrates that both platforms are sensitive to known SNVs and that few known single-nucleotide polymorphisms (SNPs) are detected by only one platform."

    2) Optimised filtering
    "To confirm that shared SNVs are indeed true variants, we used Illumina single-nucleotide polymorphism (SNP) arrays and selected all SNPs heterozygous on the SNP array."

    My question is - why are only heterozygous SNPs chosen for validation when using Illumina Omni arrays?
    Last edited by ak352; 09-16-2013, 04:53 AM.
    Please answer my unsolved question - http://seqanswers.com/forums/showthread.php?t=33740

  • #2
    Bump. Please tell me if the question is not clear.
    Please answer my unsolved question - http://seqanswers.com/forums/showthread.php?t=33740

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