search

fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
353 stars 47 forks source link

filtering normal SV from tumor SV #215

Closed mdiaz09 closed 5 months ago

mdiaz09 commented 5 months ago

When merging two VCFs is it possible to remove all lines that appear in both files using survivor, or should this be done using other tools, like bcftools?

fritzsedlazeck commented 5 months ago

There is a parameter for this in the merge command. Also there is a supp= tag in the output VCF file if you want to use that on an already merged VCF Cheers Fritz

mdiaz09 commented 5 months ago

I am having trouble finding that option in the merge command, would you mind pointing it out?

fritzsedlazeck commented 5 months ago

Sorry sure. It's the 3rd argument. Set this to eg. 2 instead of 1 So for example survivor merge files 1000 2 1 0 0 0 output.

mdiaz09 commented 5 months ago

Won't that generate an output with SVs present in both files? I am looking to remove all of the SV that overlap in the files, removing the SV from the normal file and leaving just the SVs from the tumor file.

fritzsedlazeck commented 5 months ago

Ooh sorry I misunderstood.. traveling. Yes than it's bcftools or you use the supp=1; tag.

mdiaz09 commented 5 months ago

thanks!