Type | Rep | Mapper | No. SNP |
|---|
| | | GSNAP | BWA | NextGenMap | Novoalign | Stampy | |
|---|
Known | 1 only | 13 | 3 | 7 | 3 | 4 | 13 (9,1) |
Known | 2 only | 21 | 2 | 8 | 5 | 4 | 21 (10,0) |
Known | 1 & 2 | 94 | 32 | 70 | 60 | 51 | 94 (75,0) |
Novel | 1 only | 10 | 1 | 1 | 1 | 3 | 10 (5,3) |
Novel | 2 only | 11 | 5 | 3 | 4 | 4 | 11 (2,0) |
Novel | 1 & 2 | 18 | 5 | 10 | 8 | 11 | 18 (12,1) |
- Shown is the number of SNPs in the HLA region of NA12878 that were called by GSNAP + GATK UnifiedGenotyper but missed in the public call set. The GSNAP + GATK UnifiedGenotyper specific SNPs included those only identified from replicate 1 (“1 only”), from replicate 2 (“2 only”), and from both (“1 & 2”). The number of SNPs identified by GATK UnifiedGenotyper together with the other four mappers was also shown here. The last column is the total number of SNPs, and those in SNP cluster and segmental duplications were shown in parentheses. Known SNP matching dbSNP v138; novel SNP not matching dbSNP v138, Rep replicate; HLA Chr6:29,500,000–33,500,000 bp
