Inaccurate Chain Orientation in Survivor SV Results Merging

[zhaowsong]

Dear Author,

I am currently using Survivor to merge SV results from SVaba, Delly, and Manta with the following code:

${survivor} merge ${work_dir}/${tumor}.sample_files 1000 2 1 1 0 50

My intention is to use these merged results as input files for ShatterSeek. However, I have noticed that the direction of many chains in these samples is consistently positive (+), which is clearly incorrect. Consequently, the results of chromothripsis analysis are also inaccurate. (I am working on osteosarcoma, and the chromothripsis occurrence rate is quite high.)

I would appreciate any guidance or suggestions on how to address this issue and ensure the correct orientation of chains in the merged SV results.

Thank you for your assistance.