Question about pangenome-graph-from-assemblies

eblerjana / pangenie

Pangenome-based genome inference

MIT License

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Question about pangenome-graph-from-assemblies #54

Open YuChrming opened 8 months ago

YuChrming commented 8 months ago

I want to generate a VCF file from haplotype-resolved assemblies using pangenome-graph-from-assemblies, recommended in document, but encounter error. Is it a format problem of config.json ? The pictures are error report and my json file respectively. Thans a lot!

eblerjana commented 8 months ago

In the reference section, the field has to be named "filename", you cannot change it to a custom name. This only works for the assemblies and trios section (see description in README of the respective repository: https://bitbucket.org/jana_ebler/vcf-merging/src/master/pangenome-graph-from-assemblies/)