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Table 1 Identification of independently verified, disease causative SNPs

From: BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity

SNP Atlas GATK Samtools FaSD BAYSIC
rs113994057 Detected Detected (Tranche90) Detected Not detected Detected
rs113994049 Not detected Detected (LQF) Detected Detected Detected
  1. SNP variants were detected in samples from four individuals from a single family with one individual affected with white matter leukodytrophy 2 healthy parents and a healthy sibling. For each of two causative SNPs in the EIF2B5 gene associated with white matter leukodystrophy (rs113994057 and rs113994049), the ability of Atlas, GATK, Samtools, FaSD or BAYSIC (with the default posterior probability cutoff of 0.8) to detect each variant is shown. For GATK, the most stringent filter that could be applied and still detect each variant is shown in parentheses. “Detected” indicates that the SNP was predicted for one of the four subjects.