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plink QC

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 ?

qc plink
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written by karthick • karthick

1 answer

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

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

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written by LauferVA LauferVA

thank you for your response sir

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written by karthick • karthick

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

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written by LauferVA LauferVA

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.

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updated by Ram Ram • written by karthick • karthick

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.

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written by Darwin • Darwin

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

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written by karthick • karthick

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