Table 3 Number of SNPs identified with different combinations of SNP callers and GBS references
| Â | Unified Genotyper (GATK) | Haplotype Caller (GATK) | ||||||
|---|---|---|---|---|---|---|---|---|
Ref50 | Ref50_98 | Ref70 | Ref70_98 | Ref50 | Ref50_98 | Ref70 | Ref70_98 | |
No. of GBS tags | 34,960 | 28,579 | 16,725 | 15,397 | 34,960 | 28,579 | 16,725 | 15,397 |
No. of SNPs | 2358 | 5534 | 3939 | 4477 | 1766 | 4593 | 3413 | 3934 |