Question: Snptest -overlap option
gravatar for m93
2.4 years ago by
m93180 wrote:

I am running Snptest on 2 datasets together. I used the -overlap option to make sure I tested only the SNPs common to both datasets. My code looks as follows:

/apps/snptest/2.5.2/snptest_v2.5.2 \ -data data1.imputed pheno1.sample data2.imputed pheno2.sample \ -overlap \ -o combined.snptest \ -frequentist 1 \ -method score \ -pheno pheno \ -cov_names cov1 cov2 cov3 cov4 \ -exclude_samples all_samples_exclusions_for_snptest.txt \ -exclude_snps exclude_snps.txt

Snptest documentation mentions about the -overlap option: "A restriction is that all .gen files must have SNPs in strictly increasing order of position (after SNP exclusions). If this is not the case a warning will be given."

I'm trying to check whether I have add such a warning, has anyone got an example of how such a warning might look like? I want to be absolutely sure I haven't missed it.

ADD COMMENTlink written 2.4 years ago by m93180


in what kind of format pheno file should be for this analysis?

Thanks Ana

ADD REPLYlink written 7 months ago by anamaria80
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