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micahvista / VACmap

VACmap: a long-read aligner specifically designed for complex structural variation discovery
GNU General Public License v3.0
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Compatible with pbsv #3

Open jamesc99 opened 3 months ago

jamesc99 commented 3 months ago

Hi there,

I am trying to run pbsv with VACmap as the aligner and I wonder if there is any option in VACmap where I can generate the SM tag of the read groups, associates aligned reads, which is required by pbsv.

Thanks for your time, Ryan

As ref (from PacBio pbsv): The sample name, stored in the SM tag of the read groups, associates aligned reads with a particular sample. It is required for downstream joint calling. Sample names are transferred from the RG headers to the .svsig.gz file. https://github.com/PacificBiosciences/pbsv

micahvista commented 3 months ago

Dear Ryan,

I apologize for any inconvenience you may have experienced. I'm pleased to inform you that I've addressed your concern by adding the Read Group (RG) option to VACmap. Please download the latest version of VACmap and realigning your reads, include the following additional parameters: --rg-id UNIQUE_ID --rg-sm SAMPLE_ID Replace UNIQUE_ID with a unique identifier for the read group and SAMPLE_ID with your sample name. This update should allow VACmap to generate the SM tag in the read groups, which is required by pbsv for downstream processing.

Additionally, I'd like to bring your attention to a potential limitation when using pbsv with VACmap alignments. pbsv utilizes minimap2 internally to realign sequences and detect structural variants (SVs). As a result, there's a possibility that pbsv might miss some variants that VACmap aligns correctly but minimap2 fails to align. This is a minor consideration, but it may be relevant when interpreting your results.

I'm greatly appreciate your feedback. If you encounter any further issues or have additional questions, please don't hesitate to contact me. .

Best regards, Hongyu Ding

jamesc99 commented 3 months ago

Hi Hongyu,

Thanks so much for your quick response and update!!! I will run your latest version and let you know if I have any question.

btw, I suggest you use version control in the release so that future users can report issues with specific version.

Best,

micahvista commented 3 months ago

Dear Ryan,

Thank you for your prompt and positive reply. And I want to thank you for your excellent suggestion regarding version control. You're absolutely right - implementing proper version control would indeed make it easier for users to report issues specific to each version. This is a great point that will help improve our development and support processes. I'll implement this in future releases.

Please don't hesitate to reach out if you encounter any issues or have any questions while using the latest version.

Best regards, Hongyu Ding