Xianjie Huang

Yes, you may genotype per donor and then combine the donor-wise VCF files for vireo (see [issue 100](https://github.com/single-cell-genetics/cellsnp-lite/issues/100) for detailed discussion).

Hi, thanks for the feedback. It could happen that some SNPs have OTH ratio 1 in mode 1, since the REF and ALT alleles are not inferred from data but...

Thanks for the good question. 1. Cellsnp was designed for bi-allelic SNPs. In its mode 1, REF and ALT alleles are specified by user while in mode 2, REF and...

Hi, thanks for the question. I am not quite familiar with vartrix's consensus matrix. Please correct me if my understanding is wrong. I assume it is generated by the `consensus`...

Hi, thanks for the feedback. Sometimes certain thread(s) could indeed stick for a long time when the read depth is very high. Unfortunately, it is difficult to change the framework...

To address this issue, we are thinking about two strategies: 1) split the SNP list (mode 1) or chromosome regions (mode 2) into smaller batches and push the batches into...

Hi, the files in the output folder should probably be the temporary files (with suffix such as `.0`, `.1`, ... etc). When the program finishes, the output folder should look...

The command line contains all the parameters you used to run cellsnp-lite, e.g., `cellsnp-lite -s $BAM -b $BARCODE -O $OUT_DIR -R $REGION_VCF -p 20 --minMAF 0.1 --minCOUNT 20 --gzip`. The...

Hi, searching and installing cellsnp-lite work well on my Linux HPC. Can you try installing again? or you may report the issue to bioconda. FYI, my conda version is 4.12.0...

Hi, it seems bioconda does not compile packages for `osx-arm64` platform, according to [this conda issue](https://github.com/conda/conda/issues/11216) (Feb, 2022). You may try setting up an `osx-64` (intel) conda env and then...