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Post by jfertaj on Nov 7, 2019 13:39:04 GMT
I am trying to run an analysis of SMR analysis of two molecular traits with methylation and expression. However, I always get a high percentage of allele differences between pairwise data sets (including the outcome eQTL summary data, the exposure eQTL summary data and the LD reference data)
This is the ERROR: 370895 SNPs (73.16% > 5.00%) with allele frequency differences > 0.20 between any pair of the data sets are excluded from the analysis. ERROR: the analysis stopped because more than 5.00% of the SNPs were removed by the allele frequency difference check. You can change the proportion threshold by the flag --diff-freq-prop
However, my expression and methylation have the same allele frequency, they are from the same individuals and when I check the frequency of my LD (1000 Genomes phase3 CEU) using plink: plink --bfile my1000GP3_CEU --freq, and check the differences only a few SNPs have 0.20 differences, how the program calculate the differences??
Thanks
Juan
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ax
New Member
Posts: 27
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Post by ax on Dec 6, 2019 1:32:29 GMT
Hi Juan,
Could you check if the allele order is the same in two molecular traits?
I guess if A1 is a major allele in one dataset and a minor allele in another dataset, it could cause this error.
AX
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