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10XGenomics / vartrix

Single-Cell Genotyping Tool
MIT License
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error of umi #78

Closed chenjy327 closed 1 year ago

chenjy327 commented 2 years ago

Hi, I am trying to use vartrix to analyze test data, and I have added the option of '--umi', vartrix_linux --umi -v ./test_dna.vcf -b ./test_dna.bam -f ./test_dna.fa -c ./dna_barcodes.tsv -o ./matrix.mtx but the following error occurs, 08:52:44 [ERROR] The resulting matrix has a sum of 0. Did you use the --umi flag on data without UMIs? may I ask what is the cause.

Thanks!

pmarks commented 1 year ago

Hi @chenjy327 - this is usually caused by not having any reads covering the SNPs you included in the VCF, on the barcodes you included. This can happen if there are any mismatches between genome version or between datasets. One way to check would be to manually inspect the reads in the BAM file at the SNP locations listed in the VCF, perhaps using IGV.