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DecodeGenetics / graphtyper

Population-scale genotyping using pangenome graphs
http://dx.doi.org/10.1038/ng.3964
MIT License
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SNV discovery from PacBio or Nanopore data #86

Open twesigomwedavid opened 3 years ago

twesigomwedavid commented 3 years ago

Hi @hannespetur,

Sorry I might have missed this somewhere. Does Graphtyper perform SNV discovery from PacBio or Nanopore data or is this something still under development?

Thank you

Kind regards, David

hannespetur commented 3 years ago

Hey. That is work in progress. There is currently only some very simple pileup only (no graph realignments involved) genotyping implementation for these data, using the "genotype_lr" subcommand.

Best, Hannes

twesigomwedavid commented 3 years ago

Okay, great. Thanks Hannes.

alexweisberg commented 2 years ago

Hi Hannes, I was wondering if there was any potential support for this in recent versions of graphtyper? Alternatively, would Q20+ Nanopore reads split into 150 bp fragments be compatible with graphtyper (for SNP calling), or is the error rate still too high? Thanks!

twesigomwedavid commented 2 years ago

Hi Hannes,

I tried using graphtyper_lr for variant genotyping using PacBio data—however indels were not genotyped/called. Is there an option I could supply to enable genotyping for both indels and SNPs from this kind of data using graphtyper_lr? Thanks