Identification of variants from Spatial Transcriptomics using STARSolo

Question

[kanika.151]

Hello All,

Sorry for asking a naïve question. Can we identify variants from spatial transcriptomics data by using STARSolo bam files?

We have been using snRNASeq or scRNASeq data for identifying variants.

We have been testing these pipelines:

FastQC --> STAR (two pass mode) --> GATK

FastqQC --> STARSolo --> Monopogen (idk if GATK will also work on the bam files received from STARSolo)

Do you think the same thing will work for Visium ST data? Is there any pipeline out there? Also, if you know if the bam files obtained from STARSolo can be fed into GATK to get a VCF file?

Thank you.

[GenoMax]

While anything is possible question to ask: is it logical/sound to do.

Some past threads to consider

Variant calling 10x 3' scRNA data?
Calling variants/SNP for single-cell RNA-seq data

[kanika.151]

Thank you. I actually know this but we are planning to look for common or known variants. As mentioned in this Variant calling from scRNA-seq data aids in cellular identity

So do you think a similar thing is possible via ST?

[GenoMax]

Potentially. Within the constraints noted in threads above and the technology used. R2 is an RNA read in ST.