Table 10 Pairwise comparison based on block and SNV disagreements of hg19 DP1 data
From: Pairwise comparative analysis of six haplotype assembly methods based on users’ experience
Block-Disagree | HapCUT2 | MixSIH | PEATH | WhatsHap | WhatsHap. Filter | SDhaP | MAtCHap |
|---|---|---|---|---|---|---|---|
HapCUT2 (32,150 blocks) | 0 | 459/32,150 (1.43%) | 188/32,150 (0.58%) | 1690/32,150 (5.26%) | 1690/32,150 (5.26%) | 4860/32,150 (15.12%) | 494/32,150 (1.54%) |
MixSIH (32,252 blocks) | 885/32,252 (2.74%) | 0 | 655/32,252 (2.03%) | 1924/32,252 (5.97%) | 1924/32,252 (5.97%) | 5109/32,252 (15.84%) | 664/32,252 (2.06%) |
PEATH (31,355 blocks) | 1005/31,355 (3.21%) | 976/31,355 (3.11%) | 0 | 2032/31,355 (6.48%) | 2032/31,355 (6.48%) | 5215/31,355 (16.63%) | 838/31,355 (2.67%) |
WhatsHap (10,132 blocks) | 6353/10,132 (62.70%) | 6344/10,132 (62.61%) | 6328/10,132 (62.46%) | 0 | 6602/10,132 (65.16%) | 6347/10,132 (62.64%) | |
WhatsHap.Filter (8149 blocks) | 2362/8149 (28.99%) | 2258/8149 (27.71%) | 2227/8149 (27.33%) | - | 0 | 2824/8149 (34.65%) | 2255/8149 (27.67%) |
SDhaP (32,252 blocks) | 5207/32,252 (16.14%) | 5121/32,252 (15.88%) | 5109/32,252 (15.84%) | 5702/32,252 (17.68%) | 5702/32,252 (17.68%) | 0 | 5129/32,252 (15.90%) |
MAtCHap (31,355 blocks) | 1274/31,355 (4.06%) | 954/31,355 (3.04%) | 838/31,355 (2.67%) | 2105/31,355 (6.71%) | 2105/31,355 (6.71%) | 5246/31,355 (16.73%) | 0 |
SNV- Disagree | HapCUT2 | MixSIH | PEATH | WhatsHap | WhatsHap. Filter | SDhaP | MAtCHap |
HapCUT2 (115,215 SNVs) | 0 | 8881/115,215 (7.71%) | 6190/115,215 (5.36%) | 15,960/115,215 (13.85%) | 15,960/115,215 (13.65%) | 27,098/115,215 (23.52%) | 9224/115,215 (8.01%) |
MixSIH (115,790 SNVs) | 11,034/115,790 (9.53%) | 0 | 10,153/115,790 (8.60%) | 17,307/115,790 (14.95%) | 17,307/115,790 (14.95%) | 28,183/115,790 (24.34%) | 10,240/115,790 (8.84%) |
PEATH (115,813 SNVs) | 12,872/115,813 (11.11%) | 13,671/115,813 (11.80%) | 0 | 19,263/115,813 (16.63%) | 19,263/115,813 (16.63%) | 31,494/115,813 (27.19%) | 12,508/115,813 (10.80%) |
WhatsHap (178,523 SNVs) | 165,569/178,523 (92.74%) | 165,603/178,523 (92.76%) | 165,582/178,523 (92.75%) | 0 | 166,693/178,523 (93.37%) | 165,661/178,523 (92.80%) | |
WhatsHap.Filter (115,745 SNVs) | 94,685/115,745 (81.80%) | 93,576/115,745 (80.85%) | 93,258/115,745 (80.57%) | - | 0 | 96,750/115,745 (83.59%) | 93,491/115,745 (80.77%) |
SDhaP (115,813 SNVs) | 28,693/115,813 (24.78%) | 28,261/115,813 (24.40%) | 28,253/115,813 (24.40%) | 31,441/115,813 (27.15%) | 31,441/115,813 (27.15%) | 0 | 28,452/115,813 (24.57%) |
MAtCHap (115,813 SNVs) | 15,417/115,813 (13.31%) | 13,563/115,813 (11.71%) | 12,508/115,813 (10.80%) | 19,750/115,813 (17.05%) | 19,750/115,813 (17.05%) | 31,801/115,813 (27.46%) | 0 |