I'm seeing output from PBWT that looks like this:
3 112841 rs78923776 C G . PASS RefPanelAF=0.000153988;AN=2;AC=0;INFO=1 GT:ADS:DS:GP 0|0:0,0:0:1,0,0 3 112841 rs78923776 C T . PASS RefPanelAF=0.078534;AN=2;AC=1;INFO=1 GT:ADS:DS:GP 0|1:0,1:1:0,1,0
The first line says that my genome is
CC at this position, but the second line (for the second alt allele) says that my genome is
CT at this position. OK, the first line couldn't say this, so it calls me as REF/REF, but this call has to be interpreted in the context of the second call, and can't be taken at face value.
That's why I wonder if this is valid VCF or if it's actually breaking the specification.
The line should be 'squashed' down to the following (I think):
3 112841 rs78923776 C G,T . PASS RefPanelAF=0.000153988,0.078534;AN=3;AC=0,1;INFO=1 GT:ADS:DS:GP 0|2:0,0:0:1,0,0