is this tool suitable for Creating a phased VCF of proximal variants?
gudeqing opened this issue · 1 comments
gudeqing commented
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 commented
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.