CNV calling for haplotype reference genome

Question

[katjanjarosz]

Hi! I would like to perform CNV calling for several strains of Saccharomyces cerevisiae based on data after NGS sequencing. Can anyone recommend a tool which can base on haploid reference genome and without knowledge of samples ploidy? Thanks

Answer 1

[jared.andrews07]

CNVkit should work, though it does require a normal "reference" sample(s) to base things on.

[katjanjarosz]

Thank you very much!