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?
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?
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