How to use Manta output for ShatterSeek? No Strand info, and different SVtype about shatterseek HOT 3 CLOSED

Hello, you could use e.g. mergevcf https://github.com/ljdursi/mergevcf to obtain a ShatterSeek compatible notation.
Best,
Isidro

from shatterseek.

Thanks, I understood that from the discussion in the issue section. but my second question was about the outputs from Manta, which are VCFs, so, what do I need to do we the SV-types from it and what is supported with ShatterSeek? I assume MergeVCF doesn't change anything from the VCF outputs from Manta, right? Do I need to use another tool for SV calls? if so, what would be your recommendation? Thanks

from shatterseek.

Hello, I would suggest that you try to use mergevcf as indicated above (please read the documentation) and/or convert the manta calls to the notation used in PCAWG (+/- for deletions; -/+ for duplications, etc). If you have questions about the output of manta it would be better for you to contact the developers of that tool. Hope this helps, Isidro

from shatterseek.