How to find variants which are not present in second file

Question

[shubhamkumbhar420]

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

Answer 1

[Pierre Lindenbaum]

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

[shubhamkumbhar420]

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.

[Pierre Lindenbaum]

bcftools query