How to create a SNP VCF file?

Question

[psyc_biostars]

I'm working through an example on the vargeno github page, and in their example they have a file called snp.vcf

https://github.com/medvedevgroup/vargeno/blob/master/test/snp.vcf

How would such a file be created? Would it be something you would have to write manually, or does a program generate it?

[ozankiratli]

Do you need specifically the SNPs?

Answer 1

[Jorge Amigo]

The VCF extension may be used for vCard files, but in the context of SNPs and genotyping, a minimum google search should have taken you to The Variant Call Format Specification

Answer 2

[JC]

VCFs are generally created from real data using GATK, FreeBayes, samtools/bcftools, etc.