Disable/do not consider HCV

[ammaraziz]

Hi guys,

Is it possible to disable analysis of HCV even if it is present?

This is how I am running the pipeline:

micall folder --project_code HIVB --skip trim.censor -s

[Donaim]

Hi @ammaraziz

I am thinking that the analysis that you refer to is when MiCall uses HCV as one of the reference genomes.
This is manifested by occasional presence of HCV on the genome coverage plots and in the conseq/contigs files.
Could you clarify if that is correct?

In case it is, then there is currently no way to disable this from the CLI.
But I think it could be a useful feature.
I will create a corresponding task for it.

[ammaraziz]

Hi @Donaim,

Thats correct.

It's very handy to be able to detect HCV coinfection but there are situations that would require us to not have MiCall either output or not process any HCV reads.

Is there anything I can do to the pipeline in the mean time to disable it? Eg remove the seed references?

Thanks!

[Donaim]

Hi @ammaraziz

Yes, you should be able to remove the seed references in the container, though this isn't too easy.
Reference sequences live in micall/blast_db/refs.fasta.
They are compiled into blast database during the build of container image.
So if we edit the file, then we also need to recompile the database.
That is done via micall make_blast_db.

Hope that helps for now.

[donkirkby]

What exactly are you trying to change in the output? The easiest option is to just ignore the HCV sequences in the output, and use the outputs you actually want. You could even delete the HCV results at the end if you wanted to for some reason. The hardest part would be removing HCV results from the genome coverage maps, if you care about those, but you could rerun the script to generate them after removing the HCV results, I guess.

If that doesn't work for you, then @Donaim is right that you can remove the HCV reference sequences. However, I don't think you need to touch the blast database when you're running the remapped version of MiCall. I think you only need to remove the HCV project from projects.json.

Here's an experiment for you to try:

1. Download a copy of projects.json. This does change from version to version, so you'd need to repeat this step when updating to a new version of MiCall.
2. Remove the HCV project definition. That's currently on lines 3 to 1079 of projects.json.
3. When you run MiCall under docker, bind mount your modified file to /opt/micall/micall/projects.json.
4. Do all the same steps with lines 3 to 1767 of project_scoring.json. It's possible you can skip this file, so try it both ways.

[ammaraziz]

What exactly are you trying to change in the output?

Exclude the HCV calls.

The reasoning behind this request is that we are testing for HIV only. HCV detection and analysis is considered a second, not requested, test. Which causes issues upstream. I've argued that detection is not the same as testing but I've been over-ruled.

Thanks for the detailed instructions on how to amend MiCall. I think I will opt for upstream processing to all non-HIV reads.