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

BMC Bioinformatics

Table 1 Identification of independently verified, disease causative SNPs

SNP	Atlas	GATK	Samtools	FaSD	BAYSIC
rs113994057	Detected	Detected (Tranche90)	Detected	Not detected	Detected
rs113994049	Not detected	Detected (LQF)	Detected	Detected	Detected

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.

ISSN: 1471-2105