not creating vcf file

[1064821368]

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 ?

[1064821368]

Command is: parsnp -p 8 -c -x -r NT1F31-chromosome.fa -d test/ -o NT1F31-fa/

[empiricalbayes]

I have the same issue. No vcf is generated.

[gavinmdouglas]

For anyone else confused by the lack of a vcf file in the output - see this issue: #24

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