Conditional analysis using EPACTS (which SNP identifier to use as covariates?)

[Asahi Hishida]

Hello Dear Dr. Hyun & all,

I am now working on the conditional analysis of newly found SNPs based on the 1000G-imputed GWAS, and wondering how to input/specify the reference (=top) SNP in the region in the actual EPACTS commands.

I hear we can do such conditional analyses by including the top variants as covariates, but I'm not sure which SNP identifier to use in such conditional analyses.

Here are the examples:

/bin/epacts single –vcf ./(input file name).recode.vcf.gz –ped (ped file name).ped –min-maf 0.05 –chr （chr no.） -pheno （phenotype name） -cov SEX –cov AGE –cov (SNP name: rsNo.? or MARKER ID, such as 1:15903_G/GC? )  –cov PCA1-PCA5 –test q.lm –anno –out out/test –run 2）

Sorry to bother you in this summer season, but I appreciate your kind considerstion and support!

With Best Regards,

Asahi Hishida

[Hyun Min Kang]

Use --cond [CHROM]:[POS]_[REF]/[ALT]  (or use [CHROM]:[POS] only if there are no other overlapping variant). 

Hyun.

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Hyun Min Kang, Ph.D.

John G. Searle Assistant Professor of Biostatistics,
University of Michigan, Ann Arbor MI 48109-2029

[Asahi Hishida]

Dear Hyun,

Thanks a lot for your instructive reply!

It really helps!

Best,

Asahi

2017-08-16 3:30 GMT+09:00 Hyun Min Kang <hmk...@umich.edu>:

Use --cond [CHROM]:[POS]_[REF]/[ALT]  (or use [CHROM]:[POS] only if there are no other overlapping variant). 

Hyun.

On Mon, Aug 14, 2017 at 2:11 AM Asahi Hishida <ah758...@gmail.com> wrote:

Hello Dear Dr. Hyun & all,

I am now working on the conditional analysis of newly found SNPs based on the 1000G-imputed GWAS, and wondering how to input/specify the reference (=top) SNP in the region in the actual EPACTS commands.

I hear we can do such conditional analyses by including the top variants as covariates, but I'm not sure which SNP identifier to use in such conditional analyses.

Here are the examples:

/bin/epacts single –vcf ./(input file name).recode.vcf.gz –ped (ped file name).ped –min-maf 0.05 –chr （chr no.） -pheno （phenotype name） -cov SEX –cov AGE –cov (SNP name: rsNo.? or MARKER ID, such as 1:15903_G/GC? )  –cov PCA1-PCA5 –test q.lm –anno –out out/test –run 2）

Sorry to bother you in this summer season, but I appreciate your kind considerstion and support!

With Best Regards,

Asahi Hishida

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Hyun Min Kang, Ph.D.

John G. Searle Assistant Professor of Biostatistics,
University of Michigan, Ann Arbor MI 48109-2029

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Asahi Hishida, M.D., Ph.D., M.P.H. (M.P.H. 2012, UNC Epidemiology)

Lecturer (Specially Invited), Dept of Preventive Medicine, 

Nagoya University Graduate School of Medicine

E-mail: his...@alumni.unc.edu; ah758...@gmail.com