Table 9 Comparing SNVs in 6 HA algorithms with positions in known haplotypes
From: Pairwise comparative analysis of six haplotype assembly methods based on users’ experience
HA methods | hg19.DP1 | overlap | hg19.DP15 | overlap | hg19.DP30 | overlap |
|---|---|---|---|---|---|---|
HapCUT2 | 115,215 | 43,868 (38.07%) | 96,357 | 35,930 (37.29%) | 18,824 | 3517 (18.68%) |
MixSIH | 115,790 | 44,210 (38.18%) | 96,818 | 36,211 (37.40%) | 18,885 | 3542 (18.76%) |
PEATH | 115,813 | 44,223 (38.18%) | 96,835 | 36,225 (37.41%) | 18,887 | 3542 (18.75%) |
WhatsHap | 178,523 | 97,865 (54.82%) | 152,769 | 84,094 (55.05%) | 24,628 | 7788 (31.62%) |
WhatsHap.Filter | 115,745 | 44,198 (38.19%) | 96,783 | 36,204 (37.41%) | 18,864 | 3540 (18.77%) |
SDhaP.100,595 | 115,813 | 44,223 (38.18%) | 96,835 | 36,225 (37.41%) | 18,887 | 3542 (18.75%) |
MAtCHap | 115,813 | 44,223 (38.18%) | 96,835 | 36,225 (37.41%) | 18,887 | 3542 (18.75%) |
HA methods | hg38.DP1 | overlap | hg38.DP15 | overlap | hg38.DP30 | overlap |
HapCUT2 | 100,686 | 84,197 (83.62%) | 99,572 | 83,851 (84.21%) | 63,970 | 52,185 (81.58%) |
MixSIH | 100,807 | 84,239 (83.56%) | 99,675 | 83,887 (84.16%) | 64,023 | 52,203 (81.54%) |
PEATH | 100,810 | 84,239 (83.56%) | 99,676 | 83,888 (84.16%) | 64,025 | 52,203 (81.54%) |
WhatsHap | 100,785 | 84,332 (83.68%) | 99,648 | 83,983 (84.28%) | 63,999 | 52,265 (81.67%) |
WhatsHap.Filter | 100,625 | 84,199 (83.68%) | 99,487 | 83,846 (84.28%) | 63,917 | 52,186 (81.65%) |
SDhaP | 100,810 | 84,239 (83.56%) | 99,676 | 83,888 (84.16%) | 64,025 | 52,203 (81.54%) |
MAtCHap | 100,810 | 84,239 (83.56%) | 99,676 | 83,888 (84.16%) | 64,025 | 52,203 (81.54%) |