Handling haploid cells

[haigdjambazian]

Hi, the species I am studying is haploid: Plasmodiophora brassicae (size: 24Mb) we captured single spores.

Is there an option with cellsnp-lite to have it only make calls based on a haploid organism? I think heterozygous snps don't really make sense unless we have a doublet.

[hxj5]

Hi, cellsnp-lite was designed for diploid data. For the moment, you may have to (post-hoc) filter the heterozygous SNPs.

[haigdjambazian]

Ok, thank you.