mtDNA genotyping

[RaghadShu]

Hi, Thanks for the great tool. I am running the mtDNA genotyping viginette on one multiple myeloma sample that is originally a Multiome (GEX + ATAC)

This is the variants plot I get: (notice the vmr = 0)

Can you help me understand what this means, and why is it the case? and how to choose a high-confidance threshold for the vmr in this case.

Best, Raghad

[timoast]

Can you show the variants dataframe that you're using to generate this plot?

[RaghadShu]

Yes, this is the variable sites table obtained from IdentifyVariants()

MM3_variable_sites.txt

[timoast]

I think your data might be too low coverage. It's also possible that there are not many variants present in this, as most sites seem to have mean 0 (which is the mean counts for that variant across all the cells), suggesting that most of the covered sites are the wild-type allele

[RaghadShu]

That makes sense. I would like to double-check something: my understanding is that sc-Multiome sequencing (GEX + ATAC) only sequences what's inside the nucleus for each cell. So I am wondering if it is even possible to detect any mitochondrial genome/variants (since mitochondria are not in the nucleus) in the 10X Multiome data.

It's a bit unclear to me if the variantes detected in the vignette is from scATAC-seq only or also mtscATAC-seq too.

[RaghadShu]

Hello, no response?

[timoast]

You can read the paper that generated that data here: https://www.nature.com/articles/s41587-020-0645-6

The data is generated by mtscATAC-seq

[RaghadShu]

Yes, but I am wondering if it's correct to estimate mtDNA from scATAC (like in here: https://github.com/caleblareau/mgatk/wiki/Process-mtDNA-from-CellRanger-ATAC)

[timoast]

Better to ask over there: https://github.com/caleblareau/mgatk/issues