Variant calling 10x 3' scRNA data?

Question

[scrnaresearch]

I am relatively new to the world of bioinformatics and have some novice questions regarding scRNA-seq data and variant calling. I am wondering if it is ever legitimate to call variants from scRNA sequencing data. Specifically, I would like to know whether de novo variant discovery can be done from this data. I have seen it be said that If so, can this be done in such a way that mitigates PCR bias, and protects from discovering false positive variants?

Answer 1

[jared.andrews07]

Doing this with 10X data is a pretty large challenge due to the data sparsity. Most genes may only have 1 or 2 reads aligning, and coverage across the gene will obviously be biased. This paper has some good information. In general, you will miss much, along with all the other caveats that come with variant calling in RNA-seq data.

There are ways to look at known variants (e.g. from WGS/WES on the same sample) in your scRNA-seq data, which can be useful when comparing mutation frequencies across groups/types of cells (malignant vs normal, etc). vartrix is the 10X tool made for this, and it's pretty easy to use.

[scrnaresearch]

Thanks for this. It's very helpful