Identify frameshift/ nonsense mutation

[martian-yan]

Thanks for developing such an excellent tool. To my knowledge, this is the first tool for identifying AMR mutations in fungi. It has helped me a lot in my project.

I have a question regarding the detection of frameshift and premature stop codon mutations in target genes. These types of mutations usually have a much bigger impact than missense mutations, but the tool seems to miss them.

The reason is that when miniprot outputs a translated protein sequence (.faa file), it skips over frameshifts. However, miniprot is actually able to identify such mutations, and the frameshift and stop codon events are annotated in its GFF output.

It would be a great help if this information could be incorporated into ChroQueTas—specifically, if frameshift and premature stop codon mutations could be reported in the results, perhaps in the “New Mutation” column.

Thank you again for your wonderful tool!

[nmquijada]

Hi @martian-yan

Thank you very much for your comment! We are happy that you liked ChroQueTas :)

You are absolutely right.
Right now, the information regarding frameshifts is available in the header and the cigar string of the PAF file that is the output of miniprot. You made us realize that such information might a bit "hard to find"... as such output file is stored in the tmp/ directory and the {SAMPLE}_{PROTEIN}_miniprot.tmp (e.g. fs:i:0 st:i:0 da:i:0 do:i:0 cg:Z:528M cs:Z::528 == "no frameshifts").
You are right that this information is very valuable and therefore it should be included with the main outputs of the tools. We will implement this in the next release. Additionally, we will include some documentation to interpret this information in the wiki.

Again, thank you very much. I think your suggestion will be a very nice implementation in ChroQueTas. We will let you know as soon as the next release is ready ;)

Best,
N