We selected 27 tSNPs using the Haploview implementation of Tagger on HapMap data, applying a pairwise r threshold of 0.8 with a minor allelic frequency threshold of 0.04.
For each gene or region, tagging (t) SNPs, optimized for the Illumina platform, was selected using HapMap, applying an R threshold of 0.8 with a minor allele frequency threshold of 0.04.
For instance, one might choose a minor allele frequency threshold to define what is "rare," or choose a weighting scheme for the variants (even if constant weights).
To ensure a high genotyping success rate, a minor allele frequency threshold of 0.05 in the HapMap CEU population and an 'Illumina score' of not less than 0.6 (as recommended by the manufacturer) were established in the SNP selection process.
The two common methods for filtering imputed data are to combine a minor allele frequency threshold with either the imputed information score >0.3∼0.5 (PROPER_INFO in SNPTEST) [10], [18], [20], [21], [22] or the variance ratio >0.3 (rsq_hat in MACH) [7], [10], [20], [21], [22], [23], [24], [25].
Binning of major and minor allelle frequencies in sequence data given a minor allele frequency threshold of 0.05.
Sequence data were filtered using a minor allele frequency threshold of ≤0.2% based on the NHLBI exome variant server data (computed through the ANNOVAR annotations).
BioBin produced the MLL2 gene bin with 125 total variant loci (184 total variants) at a minor allele frequency threshold of 0.05, but was not significant (p-value = 0.4718).
SNP calls were filtered for quality by restricting the marker set to biallelic SNPs, requiring genotype calls at each SNP to have a depth of coverage of six reads in each sample, implementing a minor allele frequency threshold of ≥0.2 and limiting missing genotype data to a maximum of 20% per SNP.
We used the HapMap genotype data of the Han Chinese from Beijing (CHB) and the Japanese from Tokyo (JPT) and an r threshold of 0.8 with a minor allele frequency (MAF) threshold of 0.1.
