VCF File Creator?

Question

[Magpie101]

Hi All, I have list of SNP so-ordinate positions (extracted from a journal paper) that I need to put into .vcf format. Is there any software that will allow me to do this or do I have to do it manually?

Thanks

[harold.smith.tarheel]

A VCF file contains more information than SNP coordinates (see here for specs). At a minimum, you'll need the chromosome, position, reference base, and SNP call (the other mandatory positions can be represented by '.').

Answer 1

[Magpie101]

Thanks Harold. I have all that info; if I put a file together in something like NotePad++ with the correct info, format and file ext (.vcf) should it be accepted by vcftools?

[WouterDeCoster]

Please use ADD COMMENT to reply to earlier answers, as such this thread remains logically structured and easy to follow.

You can validate a vcf using tools such as GATK ValidateVariants, which is potentially overly strict for your application.

[harold.smith.tarheel]

VCF is tab-delimited text file, so as long as it meets the minimum requirements (file format field, header line, and fixed fields) it should work.

BTW, use ADD COMMENT button to reply.