Question: How to create a SNP VCF file?
0
gravatar for psyc_biostars
6 weeks ago by
psyc_biostars0 wrote:

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?

genotyping vargeno vcf • 165 views
ADD COMMENTlink modified 6 weeks ago by Jorge Amigo12k • written 6 weeks ago by psyc_biostars0

Do you need specifically the SNPs?

ADD REPLYlink written 6 weeks ago by evolozzy40
1
gravatar for Jorge Amigo
6 weeks ago by
Jorge Amigo12k
Santiago de Compostela, Spain
Jorge Amigo12k wrote:

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

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Jorge Amigo12k
0
gravatar for JC
6 weeks ago by
JC12k
Mexico
JC12k wrote:

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

ADD COMMENTlink written 6 weeks ago by JC12k
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