Unable to accurately extract the insertion DNA sequence in INS.sigs when the reads are supplementary alignment reads.

[epi-lhe]

Hello,

Thank you for developing this fantastic tool.

I am using cuteSV to extract somatic insertion DNA sequences from INS.sigs.

However, I noticed that for all supplementary alignment reads, the extracted DNA sequences—while having the correct length—are shifted either to the left or right.

Please see the image below, where: The first line represents the correct inserted DNA sequence. The second line shows the extracted DNA sequence from INS.sigs.

I have provided a BAM file containing an example, along with the corresponding genome file, at the following link: https://nextcloud.tuebingen.mpg.de/index.php/s/SHZgreNeWjNy273

If needed, I can share my WeChat via email (my email is [email protected]) for easier communication.

I look forward to your reply.

Best wishes,
Li He

[Meltpinkg]

Hello, @epi-lhe

Thanks for reporting this issue. We have identified some errors in cuteSV that led to the incorrect DNA sequence. We are resolving it and expect to release an update within the next 1-2 days. If you have any further questions or concerns, please feel free to reach out.
Hope it will help!

Best wishes,
Shuqi