Some bases in the “REF” column are incorrect, and this occurs in INS (insertion) types.

[wk1352313]

After detecting structural variations (SVs) using the default parameters of CuteSV, I found that the bases of “REF” in some INS (insertion) events in the vcf do not match those in the reference genome. For example, in the VCF result file from CuteSV, the base at position 83708 on chromosome 01 is reported as G, while in the reference genome, it is A.What could be the reason for this?

[Meltpinkg]

Hello, @wk1352313

This problem has been fixed in the newest version (2.1.0) of cuteSV. You can install the new version via git clone https://github.com/tjiangHIT/cuteSV.git && cd cuteSV/ && python setup.py install. By the way, the new version's pip and conda installation will be available soon.

Best,
Shuqi