Meltpinkg

Hello, @CoREse Thanks for using cuteSV. The issue you mentioned above could lead to the same signatures extracted twice from the alignment. But in the clustering step of cuteSV, the...

Hello, @Akazhiel Thanks for using cuteSV. According to VCF format, the POS of variants should be 1-based. So in cuteSV, all type of variants are 1-based. Best, Shuqi

Hello, @Akazhiel The signature files that cuteSV generates is only the temporary file for outputing the detected SVs and it is not strictly BED format. For your second doubt, I'd...

Hello, Jonatan Regarding the Control sample, it is unreasonable for the missing report of the deletion. I also felt confused and I thought about several possibilities. cuteSV filters reads whose...

Hello, @Akazhiel Sorry for my delay. I have run cuteSV on two alignment files you provided via your commands and the latest code in cuteSV's GitHub. In normal file, cuteSV...

Hello @Akazhiel I got this condition that exact match for SV is important, and we didn't consider well about it in our tool. We plan to add a new parameter...

Hello @Akazhiel We add a new parameter `--remain_reads_ratio` which means cuteSV will filter part of reads which is relatively far from the variation position in the cluster. When the alignment...

Hello, @Akazhiel The deletion is not detected in normal because there are several deletion signatures between this 495bp deletion and the next 1980bp deletion, so they are clustered into one...

Hello Melissa, Thanks for pointing this out. Could you please supply a part of your data which covers the missing DUP for me to check the error? You can use...

Hello @Akazhiel , First, you can have a look at the alignment file and in the 18th column, there will be a string started with 'SA' which represents the supplementary...