2.1 years ago by
Republic of Ireland
Merge the VCFs using bcftools merge
and then input to PLINK using --vcf
or --bcf
. When inputting, I highly recommend using the flag --indiv-sort file
so that you control exactly the order of the samples. I go over an example of this, here: A: Different samples order in .ped and phynotype data files
Without the use of the sort file, PLINK will highly likely input the samples in a different order than they appear in the VCF / BCF
The order in your sort file should then match the custom FAM file that you also create, which you specify for use when you run --assoc
. I go over this, here: A: linkage disequilibrium analysis
So an entire pipeline would look like:
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 ;
plink --noweb --assoc --ci 0.95 --counts --bfile MyVars --assoc --fam MyVars.Custom.fam ;