search

genomic-medicine-sweden / nallo

A long-read (PacBio and ONT) analysis pipeline written in Nextflow
MIT License
10 stars 3 forks source link

Add support for phasing of supplementary alignments #132

Closed fellen31 closed 1 month ago

fellen31 commented 4 months ago

Description of feature

This was added in WhatsHap 2.3 (2024-05-05), might be useful for SV analysis? @J35P312

J35P312 commented 4 months ago

Great find :P. I agree, It will be really good for SV analysis! have you tried longphase?

fellen31 commented 4 months ago

No, but a proper benchmark between WhatsHap, HiPhase and longphase has been on my mind.

fellen31 commented 3 months ago

In Longphase, this is available with --tagSupplementary.

fellen31 commented 1 month ago

I misread, --use-supplementary was added in 2.3, --tag-supplementary is already implemented in the pipeline. Closing.