how to process vcf files for GWAS analysis

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4.1 years ago

Kumar ▴ 170

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

GWAS sequencing next-gen vcf • 2.3k views

ADD COMMENT • link 4.1 years ago by Kumar ▴ 170

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Please explore PLINK

ADD REPLY • link 4.1 years ago by Kevin Blighe 88k

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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>

ADD REPLY • link 4.1 years ago by Kumar ▴ 170

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

ADD REPLY • link 4.1 years ago by WouterDeCoster 47k

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