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Can you please try if the commit I just pushed fixes the issue? I could reproduce the problem only partially, the commit fixes the malformed INFO tag. However, I was not able to reproduce the incorrect FORMAT/AD values.
I hope this is not me misusing bcftools, but there seens to be an issue between bcftools norm v1.9 and v1.12 (I did not check intermediate versions).
With bcftools v1.12
bcftools norm --multiallelics -any -old-rec-tag OLD_VARIANT
becomes:Note, that AD values always get the value from the reference base. Also, the value stored in
INFO/OLD_VARIANT
refers to theG
alternate in both cases.With bcftools v1.9
bcftools norm --multiallelics -any
becomes:The text was updated successfully, but these errors were encountered: