Additional file 5: of The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool

Figure S5. VVP box plots for all ClinVar and NA12878 variants broken down by CADD scoring class. Note that in contrast to CADD’s scores for these same variants (see Additional file 4: Figure S4), VVP assigns high scores to FRAME_SHIFT and STOP_GAINED variants in ClinVar, but low scores for those same classes in NA12878. ClinVar scored as in Fig. 2a. NA12878 was scored using the observed zygosity of each variant. Score > 56 is threshold for damaging. (PDF 177 kb

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

Additional file 3: of The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool

Figure S3. Mean scores broken down by allele frequency for VVP, CADD and SIFT. Data are for NA12878 WGS. Note very non-linear nature of the VVP curve compared to CADD and SIFT. As a result, VVP will rarely assign a common variant a high score. A desirable feature for high throughput WGS-driven analyses aimed at identification of rare, Mendelian alleles. (PDF 74 kb

Additional file 4: of The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool

Figure S4. CADD box plots for all ClinVar and NA12878 variants broken down by CADD scoring class. These results help to explain CADD’s call rate on NA12878. Note that CADD assigns high scores to FRAME_SHIFT and STOP_GAINED variants in both ClinVar and NA12878. Score > 23 is threshold for damaging. (PDF 152 kb

Additional file 1: of The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool

Figure S1. ROCs for ClinVar using various VVP impact scoring schemes. Top: coding variants. Bottom: non-coding. CADD is shown for reference purposes and for ease of comparison to Fig. 2. Data and Command lines are exactly as in Fig. 2, except for alterations to VVP impact scoring as denoted. (PDF 115 kb

Additional file 1: of Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling

Supplementary results. (DOCX 12212 kb