search

stat-lab / MOPline

Detection and genotyping of structural variants
MIT License
15 stars 5 forks source link

No inversions are reported in output #9

Closed Saeideh-Ashouri closed 8 months ago

Saeideh-Ashouri commented 8 months ago

Hello.. Thank you for developing MOPline

I am trying to run it on a number of samples, the tools I used are MANTA, DELLY, CNVnator, Lumpy, and GRIDSS. I noticed that there are no inversions reported in the output of merged file for each sample.

Do you have any ideas why it is happening in my data? Is there anything I can do for it?

Thank you in advance

Saeideh-Ashouri commented 8 months ago

Hello again,

I checked the tool config file and I think I realized the reason behind that. The reason is that inversions are not considered with this specific combination of tools I used in my study. Here I post a screenshot of the part related to inversions:

Screenshot 2023-12-27 at 13 25 17

I want to modify the config file so that MOPline can report the inversions in my samples. For this, how would you recommend me modify the file for inversions?

I have another question: GRIDSS is usually used for detecting insertions too (in addition to Manta). However, in the config file, GRIDSS is not considered as a program reporting insertions. Are there any specific reason you didn't consider it for calling insertions in MOPline?

Thank you in advance

stat-lab commented 8 months ago

In your case, only overlap calls between Manta and DELLY for middle INVs and overlap calls between Manta and GRIDSS for large INVs can be detected with MOPline. The tool combination for overlap calls indicated in SVtool_pairs_config.txt is based on our evaluation results for tools' precision and recall. You can modify the combination of tools in SVtool_pairs_config.txt, but should select better combinations of tools and the minimum number of support reads (the number followed by '${tool_name}:'). Please refer to our previous paper (Kosugi et al., Genome Biol 2019) for selecting good tool pairs. I recommend adding Wham or inGAP-sv to detect INVs.

For INS, only Manat result is used for INS calling in your tool set since our evaluation suggests that GRIDSS INS calls are not useful resource for our preset tool set such as MOPline-7t. I recommend adding inGAP-sv or INSurVeyor to recover INSs.

Saeideh-Ashouri commented 8 months ago

Thank you so much for your prompt reply. Here I close this issue.