Some SNPs are not in gene

[penglbio]

I used cellSNP to identify SNP of scRNAseq. But I found a problem many SNP sites are not in gene. In my opinion, All Reads of scRNAseq should come from gene, So all SNP sites should locate in gene.

[huangyh09]

Good quesiton. It actually depends on the protocol of the sequencing, and many of them are far from the expected and return many reads mapped to integenic regions.
Also, I assume that the genome build is matched between the VCF and bam file.

Yuanhua