FAM FILE

Question

[Eleonora]

I have to do an association study with Plink and I have to use a FAM file. I have tried many times but I always get the error that not all the individuals' IDs are present. I have built the file several times but I still have problems, how can I solve it?

Answer 1

[Eleonora]

I'm using these commands:

bcftools merge ... ... > MyVars.bcf

plink --noweb --bcf MyVars.bcf --keep-allele-order --indiv-sort file MySampleListing.list --vcf-idspace-to _ --const-fid --allow-extra-chr 0 --split-x b37 no-fail --make-bed --out MyVars ;