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How to create a SNP VCF file?

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?

vcf vargeno genotyping
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updated by Jorge Amigo Jorge Amigo • written by psyc_biostars • psyc_biostars

Do you need specifically the SNPs?

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written by ozankiratli ozankiratli

2 answers

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

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written by Jorge Amigo Jorge Amigo

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

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written by JC JC

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