VCF output formats - GooglingTheCancerGenome/sv-report GitHub Wiki
The four SV callers use different nomenclature for breakpoint notation.
Nomenclature used for breakpoint orientation (from Carl's slides):
| Notation | Insertion/Deletion | Tandem duplication | Inversion |
|---|---|---|---|
| 5' to 3' | 3to5 | 5to3 | 5to5,3to3 |
| Head to Tail | TH | HT | HH,TT |
| -/+ | -+ | +- | ++,-- |
| Bracket | N[chr:pos[ chr:pos]]N | N_chr:pos_[[ or ]]chr:posN |
Interchromosomal traslocations (TRA) can have all possible orientations
Heterogeneity of SV callers: orientations
| Caller | VCF format | Insertion/Deletion | Tandem duplication | Inversion | Traslocation |
|---|---|---|---|---|---|
| Manta | 4.1 | SVTYPE=INS/DEL | SVTYPE=DUP | INV5,INV3 SVTYPE=INV | Bracket SVTYPE=BND |
| DELLY | 4.2 | SVTYPE=INS/DEL | SVTYPE=DUP | CT^=5to5,3to3 SVTYPE=INV | Bracket SVTYPE=BND |
| LUMPY | 4.2 | SVTYPE=DEL** | SVTYPE=DUP | SVTYPE=INV | SVTYPE=BND |
| GRIDSS | 4.2 | Bracket SVTYPE=BND | Bracket SVTYPE=BND | Bracket SVTYPE=BND | Bracket SVTYPE=BND |
BND: Breakend
CT = Connection Type
** INS called as DEL? (see Lumpy issue)
Information extracted from the VCF's ALT and INFO fields