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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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cellsnp-lite on data from 1 donor #106

Open astaburuaga-garcia opened 8 months ago

astaburuaga-garcia commented 8 months ago

Hi, I have one bam/barcode file per donor (cell line), and I want to get SNPs from each donor, to then be able to identify the donors in a bam/barcode file where they where multiplexed. Does it make sense to run cellsnp-lite per each donor to identify their SNPs, then merge their vcf files for vireo?

hxj5 commented 8 months ago

Yes, you may genotype per donor and then combine the donor-wise VCF files for vireo (see issue 100 for detailed discussion).

astaburuaga-garcia commented 8 months ago

Perfect, thanks!