In which step should plink be used?

Question

[felipead66]

I have read some papers that use plink in their studies for snps. I also have read plinks' documentation. I have not, though, figured out WHEN to use the plink in the process for snp identification.

Could you please give some advice on when to use plink?

[Fabio Marroni]

What do you mean by "sap identification"?

[felipead66]

typo, the correct is "snp identification"

Answer 1

[WouterDeCoster]

Plink is used after the SNPs have been called using variant calling tools such as GATK, for statistical analysis such as association testing or Hardy Weinberg equilibrium, among many more things.