Phased output

[Lionward]

Thank you for the nice tool!

was wondering since TRGT takes the phased input into account, is it possible to produce a phased output?

Are you planning to add this feature.

Regards

[tmokveld]

Hi,

TRGT can indeed use pre-existing phasing information (HP tags) from the input BAM, primarily to help distinguish between alleles with similar lengths. However, TRGT currently does not write phased genotypes in the output VCF, though support for this feature is on the development roadmap

Best,
Tom

[tmokveld]

Additionally, you can use HiPhase for now if you still want to do the phasing downstream.