I want to compare the SNPs between case and control groups. Which software should I use?
Any help will be appreciated
Any help will be appreciated
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For comparing case and control VCFs you can generate a kind of overlap comparison using this script and the utilities in vcflib: https://github.com/ekg/vcflib/blob/master/vcfmultiway.
For generating the variant calls, you have a lot of options
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Is it possibly that you may update the dead link?
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