Xianjie Huang

Hi, thanks for your feedback. Could you share the version of cellSNP and cellsnp-lite? The reason why the read counts are different: cellSNP (actually the dependent pysam) has a default...

Hi, you may look into this Biostars page "[Addin gene information to VCF file](https://www.biostars.org/p/122690/)", hope it can help.

Hi, cellsnp-lite does not check the orientation of the reads. It extracts the SNP allele from the `SEQ` field of the BAM alignments, which should always be represented on the...

Hi, Mode 2a is more suitable for small datasets. For large datasets, you may try `Mode 2b + Mode 1a`. Mode 2a does joint calling and genotyping, but it is...

Hi, the `csp_utils.R` can be used to update the three sparse matrices when a subset of SNPs is provided. The coordinates (indexes of SNPs, 1st column) in the updated matrices...

Hi, you may simply ignore the warnings about "[W::vcf_parse] Contig ...", which are produced by htslib and have little impact on the final results. For the error of "merging the...

Hi, you may follow the steps listed in the file [scripts/SNPlist_1Kgenome.sh](https://github.com/single-cell-genetics/cellsnp-lite/blob/master/scripts/SNPlist_1Kgenome.sh#L20)

Hi, thanks for the qeuestion. You may combine the donor-wise VCF files with `bcftools merge` and then pass the merged VCF to `vireo -d $DONOR_GT_FILE`. See [vireo issue 13](https://github.com/single-cell-genetics/vireo/issues/13) and...

**EDIT:** To genotype 10x scRNA-seq data in a pseudo-bulk manner with cellsnp-lite mode 1b (or mode 2b), it is recommended to subset the BAM file first, by extracting the alignment...

Specifying `--UMItag` in mode 1b still works, it should count UMIs instead of reads.