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twolinin / longphase

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[Question] Using pre-phased information for regions with low support reads #15

Closed tuannguyen8390 closed 2 years ago

tuannguyen8390 commented 2 years ago

Hi LongPhase dev team,

I wonder if it is possible to use pre-phase SNPs information to aid in SVs phasing for regions that have low read support. For example, say with another population scale, haplotype-based phasing algorithm, Eagle/Beagle for instance.

Many thanks,

Tuan

ythuang0522 commented 2 years ago

Hi @tuannguyen8390, hybrid population- and read-based phasing is not trivial. It was once considered but withdrawn as we felt the community is moving toward read-based phasing. One possible method is using population-phased VCF with haplo-read tagging. That is, you may tag long reads by running longphase haplotag with Beagle-phased VCF. The unphased SVs will be indirectly phased by flanking SNPs in proximity. IGV should reveal the phased SVs in the Beagle-tagged bam.

tuannguyen8390 commented 2 years ago

Many thanks for the reply ! Closing the ticket for now :)