plink for haploid candida auris genome

[Naama Yefet]

hi! i am running an association study on candida auris isolated derived from skin and blood to find variants associated with violence. i would like to know if plink is the right tool for that , if it can handle haploid genome and if so, what are the adaptations that need to be made? 

[Chris Chang]

You can use the --chr-set flag to specify a haploid genome.

There are some standard diploid-dataset quality control steps (--hwe, --check-sex) which don't work for haploid genomes; and they will tell you that they don't work if you try them.