Shapeit conda #2
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I've added support for Shapeit5 from Conda. It's called with SHAPEIT5_ligate and SHAPEIT5_phase_common for the RUN_SHAPEIT5_LIGATE and RUN_SHAPEIT_PHASE_COMMON methods, respectively. It still works with the static binary, but as a backup.
SHAPEIT5 can't use the index parameter, so I used bcftools to create the .csi file.
I hope it works better for new users 😄