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Yves-CHEN / DENTIST

DENTIST (Detecting Errors iN analyses of summary staTISTics) is a QC tool for summary-data-based analyses.
GNU Lesser General Public License v3.0
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Error: SNPhas variance of 0 #23

Open cwnag-c opened 8 months ago

cwnag-c commented 8 months ago

Hello，

Thank you for developing DENTIST！

Rencently, i performed DENTIST with some gwas summary statistics , some of them stopped with an error that SNP [rs182295383] has variance of 0. Should I remove this snp before performing DENTIST? or is there a function to remove snps with variance of 0 in the DENTIST？

I am extremely grateful for your assistance in resolving this issue!

Thank you, ChaoWang

--gwas-summary /content/drive/MyDrive/GCTA_format/psy.ma
--bfile /content/g1000_eur9
--chrID 9
--iteration-num 10
--thread-num 2
--out /content/drive/MyDrive/dentist/psy/psy_dentist9
Reading GWAS summary data from [/content/drive/MyDrive/GCTA_format/psy.ma].
Reserving 1 M memory for reading. 
GWAS summary data of 6247482 SNPs to be included from [/content/drive/MyDrive/GCTA_format/psy.ma].
[warning] mogan is like to be missing, but it will only be a problem when calling for it.
[info] Calculating frequencies with 2 cpus 
[info] This bed file is plink 1.0 bedfile format. (Older)
[info] chrID == 9
[info] Aligning GWAS to the reference sample assumming both files are ordered.
[info] Performing DENTIST at 266750 SNPs shared between the summary and reference data. 
[info]  At least 4096 Mb of memory is required.
...........
..18.3%[info]This bed file is plink 1.0 bedfile format. (Older)
[error] SNP [rs182295383] has variance of 0
Yves-CHEN commented 7 months ago

Thanks very much for your interest in our tools. Short answer to your questions: Yes. remove that variant. You can try Plink to remove the variant from the reference bed file or from GWAS summary. plink --exclude-snp --make-bed

Long answer:

It reports a variance of 0 for that SNP usually due to the poor imputation which led a same genotype (e.g. genotype of 1) found in all individuals. In fact, it is recommended to perform a HWE test before running DENTIST QC, in which case, this SNP will fail in the test and you can remove this usually plink as shown above.

I will consider to add more handy features into DENTIST including this one that you are wanting to have, but it will take some time. So please try plink for your timely research.