plink QC

Question

[karthick]

we perpose in identify rick factor snp in my alzhimer's disease dataset in GWAS analysis case and control study. i don't understand plink gwas, any one explain and any workflow give me. what type of qc step i'm do it. pls any one help me. which perpose use PCA ?

Answer 1

[LauferVA]

read first: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3066182/

read second: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025522/ <--- follow the steps at the end of this second manuscript

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if doing meta-analysis (GWAMA): https://www.nature.com/articles/nprot.2014.071

[karthick]

thank you for your response sir

[LauferVA]

good luck! if you hit snags its ok - just post again :-)

[karthick]

Hi, sir I have create phenotype file ,phenotype value case - 1, control- 0 ,I'm give this phenotype value. my gwas study is case/control

IID                  FID                   
SNPs_4389   SNPs_4398     1
SNPs_8878    SNPs_8878    0

This phenotype value is correct, like example phenotype file this.

[Darwin]

You don't add phenotype status to SNPs but to your sample names. And with the file you create run pheno command in plink to update it to your fam file.

[karthick]

sorry sir, i don't understand sir please explain. give me any example sir