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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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Handling haploid cells #87

Closed haigdjambazian closed 1 year ago

haigdjambazian commented 1 year ago

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 commented 1 year ago

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

haigdjambazian commented 1 year ago

Ok, thank you.