JiangTao

Thanks for the suggestion and I'll try it as soon as possible. Best Tao

Hello @Alteroldis, This is a very interesting question. cuteSV can identify the breakend which enrolled in two different chromosomes or different haplotypes of homologous chromosomes. Also, cuteSV can report the...

Hello @charliechen912ilovbash, Sorry for replying so late. It is well known that the repeat sequence would disturb the alignment and report low-accurate breakpoints on the read. SV callers collect the...

Hello @baozg, Thanks for pointing this out. Actually, cuteSV achieves assembly-based SV calling by converting the typical SV callsets to diploid-based SV callsets. That is, cuteSV generated the initial SV...

Hello @priyambial123, I want to confirm that these two alignment files are from two SMRT cells both belong to the same sample, is that correct? If so, I suggest you...

Please perform the following steps to achieve joint SV calling: 1. Run cuteSV for each sample to generate sample specific SV callsets. 2. Perform [SURVIVOR](https://github.com/fritzsedlazeck/SURVIVOR) to merge every single vcf...

Hello @AndyLy2Zy, Sorry for replying so late. If I do this work, I would 1) extract the reads supporting one INV from cuteSV output, 2) generate the consensus fragment by...

Hello @AndyLy2Zy, Actually, according to the breakpoints of the INV that cuteSV reportes, you can extract the sequence that involved in the INV from the reference genome, and modify it...

Hello @AndyLy2Zy, Please add the parameter _**--retain_work_dir**_ and check whether there are SV signatures in the directory or not. Look forward to your reply. Tao

Hello @AndyLy2Zy, Please set the parameter "--min_support" as 1 and try again. Best, Tao