I am working on 1000Genome data. I'd like to find for every population SNPs that are only found in a selected population (population private SNPs). Now, how I'd go about it is to recursively find the difference between sets of SNPs in different populations say for YRI and LWK, I'd get all the SNPs in YRI and filter out the SNPs that are shared between YRI and LWK. I'd repeat the exercise for the other populations. I tend to think that this kind of a functionality would have been implemented in one of the VCF analysis tools or genome analysis software if you know of a command or pipeline that implements this functionality please let me know. I could code up the solution but it'd save me a great deal of time if I could avoid redundancy.
Question: Population Private SNPs
19 months ago by
ThePlaintiff • 30
Cape Town, South Africa
ThePlaintiff • 30 wrote:
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6 months ago by
dawson.white • 10
dawson.white • 10 wrote:
vcf-contrast is designed to do this. http://vcftools.sourceforge.net/perl_module.html#vcf-contrast
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