parsnp not creating vcf file

[hafizmtalha]

I followed the given pipeline to create vcf file from parsnp to further use it for genotyphi.. Commands runs ok but not creating vcf file. any help ?

[gavinmdouglas]

For anyone else confused by the lack of a vcf file in the output - see this issue: https://github.com/marbl/harvest/issues/24

You need to use the related tool, harvesttools, to generate the VCF.