clair3_nova phasing

[israelAntman]

Hi,
Does Clair3-Nova perform phasing on trio samples together, or does it phase each sample separately?

[aquaskyline]

Separately.

[israelAntman]

Separately.

Why?
Phasing could be improved by using trio data.
Whatshap also has an algorithm specifically for trio-based phasing.

[aquaskyline]

trio-based phasing is a good idea but the current implementations often lead to fewer reads being phased.

the Clair3 infrastructure demands more reads to be phased, and can tolerates some reads to be incorrectly phased.