calling diploid SNVs from long reads I'd like to call diploid SNV variants from long-reads data (~80SMRTcells PacBio). 

I have generated a draft reference genome for an indivudual from a heterozygous (~4%) species (Canu+Haplomerger2). 

I can use this reference for some applications:


RNAseq mapping;
functional annotation;
duplicate detection;
synteny analysis


but not others:


analysis of compound heterozygotes; 
allele-specific expression; 
variant linkage


This is mainly why I need phasing. FYI, I tried Falcon + FalconUnzip too, but the daligner phase was just taking too much time/resources and I need to find a strategy to make it work in reasonable time (working on it).

Meanwhile, for phasing, It was suggested to use HapCUT2 - from Canu's FAQ


  (1) "Avoid collapsing the genome" in Canu to get raw diploid assembly as complete &amp; separate as possible (2) HaploMerger2 to get high-quality reference and alternative haploid assemblies (3) HapCUT2 or other phasing tools to get the high-quality haplotype assembly based on the reference haploid assembly. 


However, HapCUT2 requires the input of a diploid SNV file. Which could be done if I had short-reads data, but yet haven't found a method for doing so with in my hands just long-reads data. 

Strategies I tried to get the SNVs:


marginPhase : method paper 


but I had a issue in running it 

Clairvoyante : method paper


but I currently don't have access to suitable GPU machines to build the model - and I can't use the models provided by the authors because my organism is too different from human



Any input would be greatly appreciated!
You could try aligning your reads to the draft reference genome with for example minimap2 and calling variants with freebayes. It appears there is a protocol for long reads: https://github.com/ekg/freebayes#re-genotyping-known-variants-and-calling-long-haplotypes

Disclaimer: I have not run freebayes myself, and it may be that this is a terrible idea. I would expect that calling SNVs (Single-nucleotide variants) from PacBio reads is very challenging.  However, with enough coverage, I think it could be possible.