Add in depth information

[gavinmonahan]

Hi Suneth and Hasindu
I am using minimod within the pipeface pipeline, and had one feature request - it is currently a bit difficult to understand the full context of the modified bases without the depth at the site. Would it be possible to add in the total number of reads or the number of non-modified reads as they do in modkit column 10 and 13?
Thanks ☺️
Gavin

[hasindu2008]

Hi Gavin

Are you after the following documented at
https://github.com/warp9seq/minimod?tab=readme-ov-file#minimod-freq

5. n_called int number of reads called for base modification
6. n_mod int number of reads with base modification

[gavinmonahan]

Hi Hasindu,

Not really - I am just wondering if it would be possible to add in either the total number of reads (with and without modification) or total number of reads without modification?

The reason being, I want to work out the proportion of reads at certain loci that are methylated, if I want to do this with minimod I have to get the depth independently, whereas it is possible with modkit already.

So I would like to have for example:
5. N_called 4 reads (eg h + m mods)
6. N_mod 2 reads (eg m mods)
7. N_total 30 reads (eg depth or unmodified)

Thank you!

[hasindu2008]

Hi Gavin

Will look into this when Suneth is back from vacation in Feb.

[imsuneth]

Hi @gavinmonahan,

Thanks for opening the issue, and I am happy to implement a new feature.

However, I am a bit unclear about your requirement and the example you gave.

So I would like to have for example:
5. N_called 4 reads (eg h + m mods)
6. N_mod 2 reads (eg m mods)
7. N_total 30 reads (eg depth or unmodified)

Because both modified (prob>thresh) and unmodified(prob<(1-thresh)) bases are counted as n_called by minimod, only the ambiguous ones are ignored. This is done separately for each modification type (m and h) as explained here.

https://github.com/warp9seq/minimod?tab=readme-ov-file#modification-threshold

Are you referring to the depth as in samtool's depth output or the summation of n_called and n_mod in minimod?

Cheers!