From: Benchmarking phasing software with a whole-genome sequenced cattle pedigree
Metric | Median SEC | Median SER (%) | Median QA haplotype block length (bp) | QAN50 (bp) | ||||
---|---|---|---|---|---|---|---|---|
Scenario | 1 | 2 | 1 | 2 | 1 | 2 | 1 | 2 |
AlphaPhase1.3 | 4612 | 3548 | 0.2412 | 0.1834 | 10,653 | 55,973 | 2,505,672 | 2,719,430 |
Beagle4.1 | 2769 | 359 | 0.1404 | 0.0183 | 484 | 45,729 | 18,212,951 | 44,254,507 |
Beagle5.2 | 191 | 55 | 0.0093 | 0.0027 | 12,334 | 6,953,676 | 47,895,001 | 62,687,474 |
Eagle2.4 | 4901 | 882 | 0.2485 | 0.0451 | 172 | 161 | 5,771,337 | 22,281,097 |
FImpute3.0 | 4477 | 115 | 0.2256 | 0.0059 | 583 | 27,490 | 6,114,640 | 79,974,276 |
ShapeIT4.1 | 386 | 50 | 0.0192 | 0.0026 | 2134 | 4,738,542 | 48,437,671 | 69,002,979 |