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

tjiangHIT / cuteSV

Long read based human genomic structural variation detection with cuteSV

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Some bases in the “REF” column are incorrect, and this occurs in INS (insertion) types. #133

Open wk1352313 opened 10 months ago

wk1352313 commented 10 months ago

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? 1700143992136 1700144034033

Meltpinkg commented 10 months ago

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