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Assign donor ids to actual donor #69

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Parul-Kudtarkar opened this issue Aug 26, 2022 · 2 comments

Parul-Kudtarkar commented Aug 26, 2022 •

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Hi,
do we have a method to assign the actual donor IDs (e.g. SAMNXXX or whatnot) to the donor 0/1/2/etc. assignments from Vireo?
This is when we have donor genotype.

Thanks,
Parul

DarioS commented Nov 17, 2022

This is a major oversight for a common use case. Have you since found a better-designed software for donor labelling?

Collaborator

huangyh09 commented Nov 17, 2022

Hi, this is only possible if you have the genotypes from these individual donors.

The genotype can come from SNP array, bulk RNA-seq (or other omics) or even RT-PCR. You may consider cellsnp-lite for genotyping if it's NGS-based data.

Once you have the donor genotype, you can either put it in the Vireo's input or do it in a post step by checking the mismatch of direct genotype and demultiplexed genotype (which you can check the notebook below):
https://nbviewer.org/github/single-cell-genetics/vireo/blob/master/examples/donor_match.ipynb

Yuanhua

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