Ref and Alt switch after imputation

Question

[sxl919]

I don't know if anyone have experienced this problem before. After having my original vcf from GATK, I impute my vcf using Shapeit2 and minimac3. However, I got something strange.

Original vcf:

2 25467408 . C T 107.66 PASS .
GT:AB:AD:DP:FT:GQ:MLPSAC:MLPSAF:MQ0:PL 0/0:.:192,0:44:PASS:99:0:0.00:0:0,105,1575

After imputed vcf (Shapeit2)

2 25467408 2:25467408 T C .
PASS;GENOTYPED_ONLY AF=0.99926;MAF=0.00074 GT:DS 1|1:2.000
1|1:2.000 1|1:2.000

As you can see the Ref and Alt for some variants have switch, making it from no call all the way to calls everywhere. Why does this happen? Any way to fix it?

Thank you

[cpad0112]

For hg38, at that position, ref is T.

[Kevin Blighe]

This can occur depending on which genotyping platform was used, because these genotype different SNPs.

Also read this to gain some enlightenment about the 'reference' genomes that we use: A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.