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Number of variants obtained by each algorithm before and after filtering
| Variants | GATK HC | FreeBayes | Intersection | Unique to GATK % | Unique to FreeBayes % | Intersection % |
|---|---|---|---|---|---|---|
| Raw SNVs | 3,911,804 | 4,216,193 | 3,593,919 | 13.7 | 7 | 79.3 |
| Filtered SNVs | 3,403,728 | 3,714,842 | 3,255,217 | 11.9 | 3.8 | 84.3 |
| Raw INDELs | 814,730 | 790,178 | 580,335 | 20.5 | 22.9 | 56.6 |
| Filtered INDELs | 725,573 | 720,426 | 542,982 | 19.7 | 20.2 | 60.1 |
SNVs, single-nucleotide variants.
