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is this tool suitable for Creating a phased VCF of proximal variants? #119

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gudeqing opened this issue Oct 17, 2021 · 1 comment
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@gudeqing
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Hi, I am wondering if this tools is suitable for Creating a phased VCF of proximal variants? This is a step required by pvacseq tool:
https://pvactools.readthedocs.io/en/latest/pvacseq/input_file_prep/proximal_vcf.html

@vibansal
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hapcut2 can phase variants based on information from sequence reads, this should phase proximal variants. It also outputs a phased VCF, so it should work for your requirement.

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