obtain common SNPs
Hi I have two vcf file from two treatment. how can I obtain common snp from this two vcf file?
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a.hasankhani74 •
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Merge the files and look for positions for which both samples have a variant.
SNPs in each file was 11350. If I want to look for each position It's time-consuming. I'm looking for the fastest way I can.
Yes, of course I don't recommend doing this manually. Merge the files and filter for those positions that for both samples have been called.
how can I merge them? and how can I filter them for those positions that for both samples have been called? Are you have pipeline for these?
Have a look at
bedtools intersect.