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How to find variants which are not present in second file

Hey guys,

I have two VCF files, Now I want variants from file1 that are NOT present in file2. How can I do this?

newbieinbioinfo

vcf

1 answer

bcftools isec   -n~10  f1.vcf.gz f2.vcf.gz

Thanks for the help! Is there a way I can get output in vcf file containing all fields like chr position ID ref alt filter and INFO column. The above command only gives chr position ref and alt.

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