No vcf is generated

[empiricalbayes]

I used the tutorial data example to call SNPs. It works but vcf file is missing. Here is the command I used:

parsnp -r ./examples/mers_virus/genomes/England1.fna -d ./examples/mers_virus/genomes/*.fna -c -o test

[Bryce Kille]

Hi @empiricalbayes,

harvesttools can handle the conversion from .ggr to .vcf, however I've added that step to parsnp to make the workflow align better with the tutorial. You can now automatically generate a .vcf file in the output by running parsnp with the --vcf flag:

>$ parsnp -r! -d examples/mers_virus/genomes/*.fna --out mers_demo --vcf
>$ ls mers_demo/
parsnpAligner.ini  parsnpAligner.log  parsnp.ggr  parsnp.tree  parsnp.vcf  parsnp.xmfa

[empiricalbayes]

Many thanks @bkille