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frankvogt / vcf2gwas

Python API for comprehensive GWAS analysis using GEMMA
GNU General Public License v3.0
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alelle frequency filter is not properly #22

Closed vinod1981 closed 1 year ago

vinod1981 commented 1 year ago

It seems, allele frequency filter in vcf2gwas doesn't work properly, I am setting it q 0.02 but I can still see many SNPs with less than 0.02 MAF in final .assoc.txt files. Even I tried other filters too, and in my case it doesn't work. Please see it and let me know if I am doing something wrong.

final command: vcf2gwas -T 4 -v GT_1.vcf.gz -pf Leaf_Soil_AB_All.csv -ap -cf pca_updated_5.csv -ac -lmm -q 0.02 -o vcf2gwas/ortho_dist/ Thanks,

frankvogt commented 1 year ago

Can you try with different files/values for -q to see if the issue persists? Thanks!

vinod1981 commented 1 year ago

Dear Frank, I am using this tool since long time and observed this issue just few days back when I started analyzing my data for postGWAS analysis. I used many files and many af cutoff with -q option but the fact is that the tool is not removing them from the final gwas results '.assoc.txt' and they are making a lot of noise in the results. So, now I am removing them manually after the gwas analysis is completed with vcf2gwas. Thanks,

frankvogt commented 1 year ago

Thanks for your feedback, I will take a look and fix the issue.

frankvogt commented 1 year ago

minor allele frequency filtering is fixed in vcf2gwas v0.8.9