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
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
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?
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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.
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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 '.').