Question: Snptest -overlap option
0
gravatar for m93
3.1 years ago by
m93240
m93240 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." https://mathgen.stats.ox.ac.uk/genetics_software/snptest/old/snptest_v2.3.0.html

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 3.1 years ago by m93240

Hi,

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

Thanks Ana

ADD REPLYlink written 15 months ago by anamaria100
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