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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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Region-level quantifications #30

Open tohein opened 2 years ago

tohein commented 2 years ago

Hi,

is there currently a way to quantify allele-specific counts at the level of genomic regions rather than individual SNVs? If not, would you consider adding such a feature to a future version of cellSNP?

Thanks a lot! Tobias

hxj5 commented 2 years ago

Hi Tobias,

It's a good question. You may want to read the Methods part in the CHISEL paper and if it's what you want, cellSNP could be used as a preprocessing (pileup/genotyping) tool for the CHISEL method.

Best Xianjie