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I was wondering if you could use the toolkit to generate a separate VCF file containing only SNPs that are found at a predetermined chromosome and base pair position. I have a plink file which I want to convert back to VCF format and it seems unbelievably hard to do so I thought this may be a good way to get around that problem?
I am aware that vcftools offers this function with the "--positions " option, however for some reason I am getting far more variants than I listed and there is nothing wrong that is obvious with my listed positions/vcf file.
Thanks in advance,