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cellsnp-lite on data from 1 donor #106

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astaburuaga-garcia opened this issue Oct 17, 2023 · 2 comments
Open

cellsnp-lite on data from 1 donor #106

astaburuaga-garcia opened this issue Oct 17, 2023 · 2 comments

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@astaburuaga-garcia
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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
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hxj5 commented Oct 18, 2023

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

@astaburuaga-garcia
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Perfect, thanks!

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@hxj5 @astaburuaga-garcia