I'd like to call diploid SNV variants from long-reads data (~80SMRTcells PacBio).
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 & 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:
- but I had a issue in running it
- 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!