Xianjie Huang

Hi, I suppose this [vireo manual](https://vireosnp.readthedocs.io/en/latest/manual.html#discriminatory-variants) could be what you want.

Hi, you may use `-S` option to specify multiple bam files in mode 1a. Yes, the shared barcodes in different bam files would be treated as one single cell. To...

you could merge all barcode tsv files into one tsv file and specify with `-b` option. When merged, the order of the barcode files does not matter as cellsnp-lite can...

Hi, the barcodes in the bam files (e.g., barcode string in the `CB` tag), together with the barcodes in tsv files, are also expected to be modifed to have the...

Hi Victor, I suppose the error is probably not a cellsnp-lite issue, but a system issue that the length of the cmdline exceeds the system limits (e.g., related to `exec`...

Hi Tobias, It's a good question. You may want to read the `Methods` part in the [CHISEL](https://www.nature.com/articles/s41587-020-0661-6) paper and if it's what you want, cellSNP could be used as a...

Hi, could you share the log file, especially the "index out of range error" part you mentioned? That should be helpful.

Hi, you mentioned there were 20 extra files for each of the expected 6 output files in step 2, which indicates either cellsnp had not finished yet, or some errors...

Hi, you can use [Linux I/O redirection](https://en.wikipedia.org/wiki/Redirect_(computing)) to get the log file (i.e., run `cellsnp-lite [options...] &>log_file`), or you can directly share the terminal output of step 2.

Hi, seems the bam file is corrupted. It could be caused by errors during downloading, alignment or post-processing. You could check the status of the bam file by `samtools quickcheck`...