Assign donor ids to actual donor

[Parul-Kudtarkar]

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]

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

[huangyh09]

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