Test phasing with HapTree-X

[pontushojer]

HapTree-X has ben re-release with the ability to phase linked-reads

Berger, E., Yorukoglu, D., Zhang, L. et al. Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. Nat Commun 11, 4662 (2020). https://doi.org/10.1038/s41467-020-18320-z

It is primarily for RNA-seq based phasing but it could be worth to test as an alternative to HapCUT2. They report a much short runtime compared to HapCUT2 (10x faster!) and aslo lower switch error rate (see Table 2).

Github page: https://github.com/0xTCG/haptreex

Issue copied from FrickTobias/BLR#232