Is it expected to generate a "position x barcode" matrix?

single-cell-genetics / cellSNP

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

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Closed Griffan closed 5 years ago

Griffan commented 5 years ago

Hi, I wonder if this is the expected result? A VCF with positions as rows and droplet barcode as columns?
Just to confirm if I am using it correctly.

Thanks!

huangyh09 commented 5 years ago

Yes, it is. From v0.1.6, if you use -O out_dir instead of -o out_file, you will also have the sparse matrices.