I am trying to perform a genome-wide association on mitogenome variants (obtained from GATK-Mutect2) vs. phenotypes by using GAPIT. The number of individuals is seven and GAPIT function does not work due to the low number of indvs. We have increased the number of the same genotype (vcfs) and phenotype files by basically copying-pasting them under different names and run the function. Would this method affect the results in any way? Is there any other way to increase the number of individuals for GWAS studies?
Hi,
I think software may not identify the copied values and therefore they may affect the results. I am thinking about it because while doing the analysis, we have to indicate the number of markers data and the number of phenotypic data. If we insert the same number of data in software, they will analyze the data and give the results. It is just my thinking and it may be wrong.
Dear Muhammed,
First, 7 individuals for GWAS is very low because you can't capture a good amount of genetic diversity using only 7 individuals. Assume, for a given SNP, all 7 individuals are A/A, so you don't have any variation for this SNP to perform association analysis. However, I think the duplication of individuals shouldn't change the result. Because it doesn't change the mean and variation of observations within each genotype group (but I'm not completely sure).
As a recommendation, first, using a loop in R (etc), remove SNPs without variation, also remove SNPs that have only 1 or 2 observations in a genotype group (both should be removed). Your remained SNPs have at least 3 observations in remained genotype groups. Now, you can perform an association study (even using lm or anova). However, this method can not compensate for the low number of individuals but it may be a bit better than the original data.
Regards.
You copy-paste the same records with different individual names. Therefore, the software considers the most frequent/exact values in different individuals. It adversely influence of the validity of your results.
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