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obtain common SNPs

Hi I have two vcf file from two treatment. how can I obtain common snp from this two vcf file?

rna-seq
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written by a.hasankhani74 0

Merge the files and look for positions for which both samples have a variant.

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written by WouterDeCoster 4.8K

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.

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written by a.hasankhani74 0

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.

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written by WouterDeCoster 4.8K

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?

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written by a.hasankhani74 0

Have a look at bedtools intersect.

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written by ATpoint 9.1K

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