4.6 years ago by
I wrote a tool that can do association testing for binary traits:
We have been using it on bacterial samples where we have multiple bacterial pools for each phenotype.
Here is a command that would work for you:
pfst --file your.vcf --type PO --target 0,1,2,3 --background 4,5,6 > out.txt
type: PO means that the genotype calls in the VCF file are for pooled data.
target: The zero based index for one phenotypic group (1,2,3,4 genotype columns)