How are the values in phasing.txt from vcfeval calculated?

[s m]

I've checked the manual for an explanation - apoloigies if I missed it. I was wondering exactly how the 'Correct/Incorrect/Unresolvable phasings' are calculated in the phasing.txt output file from vcfeval.

Thanks.

[Len Trigg]

Hi,

Actually, that output is from some early code that we were working on to summarize phasing discrepancies, however it's not clear that it's a useful computation and it should probably be removed. The gist of it is that since vcfeval effectively chooses a phasing of all heterozygous calls during the matching process, if you have a phased baseline you can work out where the calls have had to employ a discordant phasing in order for the variants to match.

Cheers,

Len.

On Tue, 12 Oct 2021 at 08:57, s m <samcm...@gmail.com> wrote:

I've checked the manual for an explanation - apoloigies if I missed it. I was wondering exactly how the 'Correct/Incorrect/Unresolvable phasings' are calculated in the phasing.txt output file from vcfeval.

Thanks.

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