Table 4 Variant quality per study-capture combination
From: Human whole-exome genotype data for Alzheimer’s disease
Study | Capture Kit info | % of variants that are monomorphic | % of non-monomorphic sites, in capture kits | Within the capture kits, % with GATK PASS | Within the capture kits, % with VFLAG 0 |
|---|---|---|---|---|---|
MIAMI family | Agilent WES v3 capture region | 97.65 | 63.22 | 97.56 | 91.70 |
MIAMI family | Agilent WES v4 capture region | 97.88 | 57.95 | 95.29 | 72.50 |
CBD | Agilent WES v5 capture region | 94.20 | 68.74 | 98.09 | 95.30 |
FASe family | Agilent WES v5 capture region | 93.60 | 70.88 | 97.57 | 91.84 |
ADGC AA | Agilent WES v6 capture region | 71.92 | 73.71 | 97.56 | 94.81 |
Knight ADRC | IDX xGen Exome Whole-Exome Research Panel v1.0 w/Custom Spike-in Baits | 95.90 | 47.79 | 97.44 | 95.48 |
ADSP-Discovery | Illumina Rapid Capture Exome (ICE) kit | 77.87 | 54.20 | 97.90 | 93.87 |
FASe family | Nimblegen VCRome sequencing w/Custom Spike-in Baits | 96.06 | 46.57 | 96.73 | 93.86 |
Knight ADRC | Nimblegen VCRome sequencing w/Custom Spike-in Baits | 91.67 | 47.97 | 97.56 | 95.31 |
ADSP-Discovery | Roche Nimblegen’s VCRome v2.1 | 69.64 | 66.22 | 98.51 | 94.69 |
FASe family | Roche Nimblegen’s VCRome v2.1 | 95.91 | 62.59 | 96.95 | 91.74 |
PSP | Roche Nimblegen’s VCRome v2.1 | 92.47 | 59.10 | 95.60 | 84.13 |
Brkanac | Roche SeqCap EZ Exome Probes v3.0 Target Enrichment Probes | 97.17 | 64.59 | 97.45 | 91.17 |
Columbia WHICAP | Roche SeqCap EZ Exome Probes v3.0 Target Enrichment Probes | 67.19 | 78.37 | 97.39 | 93.90 |
