I used bcftools merge to merge 2 VCF files, however, when I see the merged VCF file, I don't see the updated fields. Suppose if I am running 2 samples in 1 VCF file which are different and 2 samples in another VCF files. I combined them but I am not getting the updated FORMAT, INFO fields of VCF file. In that case NS should show as 4 and other fields like DP, RO,AO should be recalculated. How to handle this?
bcftools merge vcf1.gz vcf2.gz > output.vcf I tried to merge it but how would I get the updated fields.