vcftobedpe does not give strandedness for MANTA Outputs

hall-lab / svtools

Tools for processing and analyzing structural variants.

MIT License

149 stars 54 forks source link

vcftobedpe does not give strandedness for MANTA Outputs #330

Open think-o opened 4 months ago

think-o commented 4 months ago

Hi! I have been trying vcfToBedpe on my MANTA outputs. I also need strand information to be used with ShatterSeek downstream. But both STRAND_A and STRAND_B have ".".

Would be great to know how the strand info can be added

I also want to use vcftobedpe on GRIDSS-GRIPSS outputs. Does it work on the GRIDSS SV caller outputs?

samreenzafer commented 3 weeks ago

Same issue here, and then consequently the bedpeToBed12 is not working because of this. Did you figure this out?