I am working with Hi-C data generated using two 4-cutters. I have seen that there are tools to do genotype phasing from this data (HapCUT2) but this tool needs an input genotype calls VCF to work.
Has anyone performed genotype calling on Hi-C data before? I have heard that this is possible, but obviously the reads are not completely unbiased. First of all I guess they should be analysed as unpaired reads because they might connect regions that are very far away. Secondly they might also introduce a bias in the mapping as they would have a re-ligated restriction site in the reads, which might be recognized as a mutation. I guess that could be solved by very heavy trimming, as the possible motifs are known.