How to create a SNP VCF file?
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17 months ago

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 • 854 views
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Do you need specifically the SNPs?

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Entering edit mode
17 months ago

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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17 months ago
JC 13k

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

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