Does running Vireo in linux without a genotype file require the sparse matrix to be in vcf format?

[alexisweber]

I am attempting to run vireo to demultiplex my single-cell RNA-Seq data (2 donors). I do not have genotype data. I have converted my counts data to a sparse matrix, with corresponding barcode.tsv and gene.tsv files and saved them in a folder on my Desktop, cellSNP.

I am attempting to run the command provided in the manual to demultiplex the samples:

vireo -c $CELL_DATA -N $n_donor -o $OUT_DIR

I was under the impression I could submit this command where $CELL_DATA is the folder name "cellSNP" that contains my sparse matrix as indicated by the options menu: -c CELL_DATA, --cellData=CELL_DATA The cell genotype file in VCF format or cellSNP folder with sparse matrices.

However, when I run this command, I receive the following error: FileNotFoundError: [Errno 2] No such file or directory: 'cellSNP/cellSNP.base.vcf.gz'

Do I need to add a special command to run it with just the sparse matrix? Or do I need to convert my sparse matrix of single cell GEX data to vcf?

Here is the command I ran specifically: vireo -c cellSNP -N 2 -o 'outs'

any help will be greatly appreciated, thank you!

[huangyh09]

Hi,

Have you have run cellsnp-lite on the sample already? If yes, you should see files like this folder: https://github.com/single-cell-genetics/vireo/tree/master/data/cellSNP_mat

Otherwise, you could run it and re-try. If you still have the problem after that, you could share the file list in that folder.

Yuanhua