pipeline/software/script to connect (whatshap) VCF phase blocks with Hi-C reads
I have a phased vcf file (generated by whatshap) of a diploid plant species. Each chromosome holds many separate phase blocks, and I want to connect these blocks/phases with Hi-C reads that I have from the same plant, in order to extend these phase blocks.
Does anyone know if there is a pipeline which I can use to do this?
I have searched a while, and until now still without a proper solution
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