Table 1.
The number of variants that were excluded after implementing automated clustering guidelines in Illumina GenomeStudio. We compared criteria of the CHARGE consortium with adjusted criteria in our study using Korean samples. The total number of SNVs was counted with redundancy. Different categories of our guideline are shown in boldface.
| Type | CHARGE consortium guidelines | Our guidelines | ||
|---|---|---|---|---|
| Criteria | # of SNVs | Criteria | # of SNVs | |
| Clustering errors | Call Freq 0.95~0.99 | 2,841 | Call Freq 0.95~0.99 | 2,841 |
| Cluster Sep < 0.4 | 693 | Cluster Sep < 0.4 | 693 | |
| AB Freq > 0.6 | 1 | AB Freq > 0.6 | 1 | |
| AB R Mean | 645 | AB R Mean | 645 | |
| Het Excess > 0.1 | 13 | Het Excess > 0.1 | 13 | |
| Het Excess < −0.9 | 17 | Het Excess < −0.9 | 17 | |
| MAF < 0.0001 & Call Freq ≠ 1 | 119,896 | MAF < 0.0001 & Call Freq < 0.99 | 2,171 | |
|
| ||||
| AA cluster error | AA T Mean 0.2~0.3 | 759 | AA T Mean 0.2~0.3 | 759 |
| AA T Dev > 0.025 | 2,195 | AA T Dev > 0.025 | 2,195 | |
| AA Freq = 1 & Call Freq < 1 | 43,012 | AA Freq = 1 & Call Freq < 0.99 | 561 | |
|
| ||||
| AB cluster error | AB T Mean 0.2~0.3, | 847 | AB T Mean 0.2~0.3, | 847 |
| AB T Mean 0.7~0.8 | 2,685 | AB T Mean 0.7~0.8 | 2,685 | |
| AB T Dev ≥ 0.07 | 272 | AB T Dev ≥ 0.07 | 272 | |
| AB Freq = 0 & MAF > 0 | 70,597 | AB Freq = 0 & MAF > 0.0002 | 11,572 | |
|
| ||||
| BB cluster error | BB T Mean 0.7~0.8 | 690 | BB T Mean 0.7~0.8 | 690 |
| BB T Dev > 0.025 | 2,742 | BB T Dev > 0.025 | 2,742 | |
| BB Freq = 1 & Call Freq < 1 | 16,352 | BB Freq = 1 & Call Freq < 0.99 | 92 | |
|
| ||||
| Total # of SNVs | 264,257 | 46,076 | ||
SNV: single nucleotide variation; MAF: minor allele frequency.