Tools to call structural variants in haploid yeast from WGS data

Question

[Tasneem Fetian]

Hello,

I have Illumina short-read PE (2x150bp) whole-genome sequencing data from Saccharomyces cerevisiae. I have ~40 samples from different mutants and I want to call the structural variants (SV) that are in the mutants but not in their corresponding wildetype strains (background).

I already have a working pipeline to call single nucleotide variants and Indels. However, I'm having trouble finding the best way to call structural variants (larger deletions or insertions, inversions, duplications, CNVs) Many of the SV callers out there are optimized for handeling diploid human genomes. Is there any particular caller/pipeline that you would recommend for SV calling in haploid yeast?

P.S. I'm using an HPC cluster to run all of my analyses and I'd prefer not having to pull docker images due to lack of administrative privileges.

Answer 1

[Tasneem Fetian]

Updates for future visitors since there are no answers yet...

breseq is an amazing tool for variant calling in haploid genomes! The documentation and usage details are excellent. https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/index.html

Delly structrual variant caller performed decently as well. It successfully called some test deletions. However, it ran into some problems with a more complex translocation situation. https://github.com/dellytools/delly?tab=readme-ov-file

Answer 2

[clealk]

If you haven't tried dysgu yet, it should work well with haploid data https://github.com/kcleal/dysgu It also has option for working with cohorts