How to get VCF file from 10x Genomics 3' gene expression multiplexed library?

statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq

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How to get VCF file from 10x Genomics 3' gene expression multiplexed library? #88

Closed kushalsuryamohan closed 2 years ago

kushalsuryamohan commented 2 years ago

Hello, We are attempting to do the analysis from your Nature paper on demuxlet (to deconvolute multiplexed samples). The analysis requires a VCF file and I am not quite sure how to get this from 10x 3' gene expression data. Can you please provide more information on how to start from the output of 10x genomics' cellranger count output?

Thanks!

hyunminkang commented 2 years ago

You need to have separate DNA genotyping