Fig. 1

Diagram of the methodological steps of the input, internal processes and output of the “functional single nucleotide polymorphism discovery” (fSNPd) program. Legend: The first step is the ascertainment of a cohort of individuals with the phenotype to be studies; blue box. The second step is to perform exomes (with the same capture and sequencing methods) on a number of the cohort individuals; blue box. The top-most black box shows the input to fSNPd; number of individuals, number of males and females, and each individuals vcf (and if required, bam + bam.bai) files). Entering the number of males and females allows fSNP to internally check that it has assigned sex correctly to each sample, so that SNPs on the X chromosome have correct allele frequencies calculated. A second lower-most black box shows the output of fSNPd, the list of SNPs where the allele frequency is statistically altered compared to the 1000 Genomes or Exome variant Server European library data. Between the black boxes are shown the processes performed within fSNPd