I'm trying to remove an individuals from a multi-sample vcf file using bcftools and vcftools, but none of them worked well.
Also, in this file, there is no variant information at all sites for this individual (actually there is just one empty column), but this individual used for the calculation of "AN" in the INFO filed.
I used bcftools with
bcftools view -s indv26 file1.vcf -o out.vcf, it gave me the error "Number of columns does not match the number of samples", which is right as I explained above the empty column). In addition, I used vcftools with
vcftools --vcf file2.vcf --remove-indv indv26 --recode --recode-INFO-all. It removed the individual of interest, but it didn't update AN in the INFO filed. Could you please help me out what shall I do?
Sorry, the corresponding variant of the removed individuals also will be removed from the multi-sample vcf file, yes?