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.
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.