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AKT PCA....Bad genotypes #41
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It could not parse the genotype filed at that position. What does |
1 758351 1:693731 A G . PASS AF=0.12008;MAF=0.12008;R2=0.57058;AN=6762;AC=1299 DS 0.037 0.766 0.036 0.078 ...... It looks normal, so I am very confused!!! |
The software requires the |
You could convert your dosages to hard genotypes but I think you would be better off running PCA on the microarray genotypes rather than imputed ones. |
One way I am doing is to convert vcf dosage file to plink format, but it will lose some information because it will round dosage values to 0,1,2. I do not know whether there is a better way..... Thank you so much! |
PLINK1.9 also has fast randomized PCA routines these days and may be a better choice. |
Hi,
When I used
akt pca
, I got such messageMAF lower bound: 0
Thin: 1
Number principle components: 20
Reading data...
984 samples
Bad genotypes at 1:758351
Ca you explain to me what does "Bad genotype" mean in the message? How should I handle with this issue?
Thank you!
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