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vibansal / HapCUT2

software tools for haplotype assembly from sequence data
BSD 2-Clause "Simplified" License
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Convert block file to vcf after pruning #131

Open pdimens opened 1 year ago

pdimens commented 1 year ago

Good afternoon,

I see there is a method for manually pruning blocks with the python script provided, which is great. Is there a way to convert a blockfile to VCF after pruning? I haven't been able to identify a feature to accomplish that.

vibansal commented 1 year ago

The whatshap tool (https://whatshap.readthedocs.io/en/latest/guide.html) has a subcommand (hapcut2vcf) for converting a hapcut output file to a VCF file.