graphtyper SNV discovery from PacBio or Nanopore data

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

Jul 27 '21 22:07 twesigomwedavid

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

Jul 28 '21 13:07 hannespetur

Okay, great. Thanks Hannes.

Jul 28 '21 14:07 twesigomwedavid

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!

Sep 08 '22 22:09 alexweisberg

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

Nov 13 '22 11:11 twesigomwedavid