Entering edit mode
2.9 years ago
Babbala
•
0
Hi, i just imputed some SNPs using IMPUTE2, i pruned them and then kept all the haplotypes with probabilities higher than 90% (thresholding was done using Plink1.90)
but what i get is that some SNPs that do not pass the threshold are undefined with the symbol ./. (instead of the normal 0/0, 0/1 or 1/1)
I don't know if what i am doing is right and i need some advice on how to handle them because i would like to keep as much SNPs as possible and not removing samples.
I am new about imputation so any feedback is appreciated.
Thank you.
Can you please show the code that you have used for pre-phasing, imputation, and then post-conversion of the imputed data to VCF?
./.
means that, while a variant at this position was called in one or more other samples in the dataset, in the sample with./.
there was not enough information to make any call, usually no aligned reads.