generating VCF for REGION_VCF from RNA-seq data

[gebdu]

Hi,

This is more naive question as I do not have experience in SNPs.

I have 2 cell-lines scRNAseq data, combined sequenced. Now would like to separate using cellSNP (& vireo).
I got bulk RNA-seq data for this 2 cell-lines. So, question is how to make VCF file for REGION_VCF option?

thanks,

[hxj5]

Hi, you may call SNPs from (merged) bulk RNA-seq data to generate the VCF for REGION_VCF option, e.g., with samtools or cellsnp-lite mode 2b, and then pileup the scRNA-seq data with the VCF file.