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RajLabMSSM / AMP_AD_StructuralVariation

Repository for the AMP-AD structural variation manuscript
MIT License
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30X whole genome sequencing #2

Open Qijie0615 opened 1 year ago

Qijie0615 commented 1 year ago

Dear Team: Thanks for sharing the SV pipeline. Now, we have 30X whole genome sequencing. We would like to know the coverage of your whole genome sequencing. Can we apply this SV pipeline to our dates? What issues should we pay attention to?

ricardovialle commented 1 year ago

Hi, Our data was about the same coverage (30x) so the pipeline should work fine. The code included here can be fairly complicated to run, I recommend you to try our snakemake pipeline: snakeSV. Most of the same callers used here are available there, but the genotyping approach is done with GraphTyper2 instead of SVTyper (used originally). Please let me know if you have any questions or issues.

Best, Ricardo

Qijie0615 commented 1 year ago

Thank you for your quick reply. At this stage,we are testing the pipeline.