How to use WES data as a reference for genotyping and classifying single-cell data?

wheaton5 / souporcell

Clustering scRNAseq by genotypes

MIT License

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How to use WES data as a reference for genotyping and classifying single-cell data? #190

Open suhuanhou opened 1 year ago

suhuanhou commented 1 year ago

I have WES data and single-cell data (bam files, barcodes, UMIs, etc.), but I am unable to install Singularity and can only perform matching through step-by-step execution. However, I am not familiar with the specific usage in the tutorial, so I hope the author can provide some simple reference methods for me. Thank you very much!

wheaton5 commented 1 year ago

There is an option --known_genotypes where you can give it a vcf file with the genotype calls for each individual.