A simulated 26-member, 7-generation pedigree.

<p>Green symbols indicate founders that were sequenced by CGI, and purple ones indicate children whose genotyping were simulated. The topology of the pedigree was chosen to enable testing of diverse relationship estimations.</p

GRAB Workflow.

<p>GRAB Workflow.</p

Computation time in minutes for GRAB and other methods on sets of whole-genome sequences, using standard input data formats.

<p>Time spent on transforming data formats is ignored. In this example, we expended 82 minutes to phase 13 individuals by BEAGLE (excluding any markers with a no-call rate greater than 5%). More accurate phasing would require more individuals and longer time.</p

Additional file 1: of VARPRISM: incorporating variant prioritization in tests of de novo mutation association

Contains: Supplementary Methods, Tables S1–S3, and Figures S1–S3. (DOCX 389 kb

Fraction of correct predictions for real families.

<p>Values in parentheses are the percentage of predictions within one degree of the true relationship.</p

IBS percentage in different relationships of simulated families.

<p>For this visualization, the sequencing error (SE) parameter was set to zero. (A) Distribution of P2 in an example sibling pair. Siblings have much of the genome that is easily detectable as IBD2, which GRAB detects through a large number of windows with a very high P2 statistic. (B) Number of identity windows (IWs) between pairs of individuals, decreasing with increased relationship degree. (C) Percentage of contiguous IWs. A contiguous IW is any IW adjacent to another IW. Unrelated individuals have fewer contiguous IWs than relatives. (D) Maximum length of a set of contiguous IWs. This length tends to be shorter in distant genetic relationships than close relationships. IT: identical twin. FS: full sibling. PO: parent offspring. UN: unrelated individuals. UD: unknown distance.</p

Performance of (A) PLINK and (B) KING on true families.

<p>Reported relationships are illustrated by different colors. PLINK's output Z0 P(IBD = 0) and Z1 P(IBD = 1) are plotted, KING's output IBS0 (proportion of zero IBS) and kinship coefficient are plotted. Relationship must be estimated by visualization of the clusters in the graph.</p

Fraction of correct predictions for simulated families.

<p>P0_cutoff is set based on per-SNV error rate. Values in parentheses are the percentage of predictions within one degree of the true relationship.</p

Comparison of multiple relationship estimation methods on real WGS families.

<p>Values in the table are the percentage of correct predictions. Values in parentheses are the percentage of predictions within one degree of the true relationship.</p

Additional file 2: of The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool

Figure S2. Violin plots for the ClinVar dataset. Scores have been normalized as in Fig. 3. Note how the VVP benign and pathogenic scores are better separated. (PDF 157 kb