vcftobedpe does not give strandedness for MANTA Outputs

[think-o]

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]

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