Manta default calls INV as BND -- May need post-processing

[WuSelina]

Description
In the current version of call-sSV and by default for Manta, INV (inversions) are reported as breakends by default. For a simple reciprocal inversion, four breakends are reported and share the same EVENT INFO tag, and there MAY be a small tag noting the BND is an INV. The developers note we can run a supplementary script to reformat the inversions to type INV, but they chose this updated formatting because it better represents the complex nature of inversions in real genomic data, where partial inversions and complex rearrangements are more common than reciprocal events, especially in tumor genomes.

They provide the script and a brief explanation here.

There is already this discussion post for call-sSV here.

I am not sure if we should automatically run the supplementary reformatting script for inversions, but I think it is important for users to know that inversions called by Manta are not obviously noted as INV in the ID or SVTYPE fields by default.

Pipeline release version: v6.1.0

[tnyamaguchi]

I think we can provide both versions without any issues.