Call SV in multiple sample

[lg10is1]

Hi, Thanks for your helpful tools of cuteSV. I am wondering how I can use the cuteSV to call SV in multiple sample. It seems only can call SV in one sample at same time.

[Meltpinkg]

Hi, @lg10is1

cuteSV calls SV in one sample at one time. To call SV in multiple sample, you can follow this step-by-step procedure:

1. Run cuteSV for each sample to generate sample specific SV callsets.
2. Perform SV merging tools (such as SURVIVOR) to merge every single vcf into merged.vcf.
3. Rerun cuteSV for each sample with -Ivcf merged.vcf (force calling step).
4. Perform SV merging tools (such as SURVIVOR) again to merge every force called single vcf into final_merged.vcf.

Hope it will help!

Best, Shuqi