Is is possible to create a VCF file were phased variants are merged to haplotypes?
Say I have a reference genome that exists only of T nucleotides and I have the following 2 phased variants.
Chr_01 18 T G GT 0|1 0|1 Chr_01 20 T G GT 0|1 0|0
Is there then a tool that can create a VCF file were all phased variants are merged to haplotypes? For the above case that would create this variant I think?
Chr_01 18 TTT GTT,GTG GT 0/2 0/1
If there is a tool that can do the above, does that mean that the conversion of haplotypes to allelic primivites with GATK VariantsToAllelicPrimitives and vcflib vcfallelicprimitives is always reversible given the SNP phasing information?