Converting cellsnp-lite outputs to vartrix's consensus matrix

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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Converting cellsnp-lite outputs to vartrix's consensus matrix #114

Open mdmanurung opened 10 months ago

mdmanurung commented 10 months ago

Dear author,

Could you give a pointer on how to construct vartrix's consensus matrix given the outputs from the cellsnp-lite? Is it possible?

Thanks in advance!

hxj5 commented 10 months ago

Hi, thanks for the question. I am not quite familiar with vartrix's consensus matrix. Please correct me if my understanding is wrong. I assume it is generated by the consensus mode of the --scoring-method (-s) option. It seems possible to convert the cellsnp outputs based on vatrix's scoring rules. You may try using the functions in the notebook "scripts/post_hoc/subset_with_minAD_issue108.ipynb" to help load and save cellsnp output.