how to process vcf files for GWAS analysis

Question

[Kumar]

Hi, I have got vcf files from GATK. I have a total of 195 vcf files. Please let me know how to proceed for GWAS analysis. I have a phenotype file. Please suggest any method or workflow.

Phenotype file example:

Samples gender  status
 FA2001 M   affected
 FA2002 M   affected
 FA2003 M   unaffected
 FA2004 F   affected
 FA2006 F   unaffected

[Kevin Blighe]

Please explore PLINK

[Kumar]

Hi, I am new in this study. If you could elaborate steps, it would be helpful. I am using PLINK, it generates .bed,.bim, .fam with the following command.

./plink --vcf <filename> --keep-allele-order --allow-extra-chr 0 --make-bed --out <filename>

Furthermore, I tried the following command:

./plink --bfile <filenames> --recode --tab --out <output filename>

[WouterDeCoster]

The documentation of plink is excellent. Show some effort and start reading.