Question: Merge phased SNP variants to haplotypes? And is vcfallelicprimitives reversible?
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gravatar for William
4.1 years ago by
William4.7k
Europe
William4.7k wrote:

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?

vcf • 1.5k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 4.1 years ago by William4.7k
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