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single-cell-genetics / cellSNP

Pileup biallelic SNPs from single-cell and bulk RNA-seq data
Apache License 2.0
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Some SNPs are not in gene #18

Open penglbio opened 3 years ago

penglbio commented 3 years ago

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 commented 3 years ago

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