SVs calls among output files

[l0ka]

Hi,

I run AA (really nice tool, thank you!) and I was wondering if it's possible to get a bedpe file with the SVs calls, from point 2) of the algorithm ("SV detection: Detect copy number changes and structural variations using coverage and discordant read pairs within each amplicon) - or in which output file I can find this information. Basically, I'm curious to compared those SVs calls with the calls made by another tool. Thank you in advance.

[jluebeck]

Hi,

Thanks for reaching out. If you apply AmpliconClassifier to your AA outputs, one of the output files summarizes the discovered SVs (see the [sample_name]_SV_summaries directory in the AC outputs). The format will be fairly close to a .bedpe format. It's probably worth noting that AA is designed to detect amplified SVs, and will not consider unamplified SVs.

We recommend using AmpliconSuite-pipeline to wrap the data preparation, AA, and AC steps together as it uses our best practices and simplifies the interpretation of the outputs. Please let me know if you have any questions about using this.

Cheers, and best of luck with the comparisons! Jens