This is one of the SV hits: as you have stated in the docs looking at the BP notation, it is a "Deletion like".
Could you be more specific how it can be a deletion like event since there is information of 2 chromosomes (CHROM=chr 11 and ALT=chr9 present).
Even other events like "both the inversions" and the "duplication like" have similar cases
2) How the actual "Translocations", inter and intra chromosomal translocations, are interpreted by the tool?
3) What is the difference between head-to-head Inversion and tail-to-tail inversion
I have been working with SAVANA now and I would like to have more insight on these cases.
1) chr11 168863 ID_791864_1 G G[chr9:74997630[ . PASS SVTYPE=BND;MATEID=ID_791864_2;NORMAL_SUPPORT=0;TUMOUR_SUPPORT=3;SVLEN=0;BP_NOTATION=+-;ORIGINATING_CLUSTER=b29d7219f036483f8543583a7d93a420;END_CLUSTER=a75da1edbf504cd6acade698b45a39f4;ORIGIN_STARTS_STD_DEV=2.83;ORIGIN_STARTS_MEDIAN=168863;ORIGIN_EVENT_SIZE_STD_DEV=0.0;ORIGIN_EVENT_SIZE_MEDIAN=1;ORIGIN_EVENT_SIZE_MEAN=1;ORIGIN_UNCERTAINTY=3.83;ORIGIN_EVENT_HEURISTIC=0.0;END_STARTS_STD_DEV=0.0;END_STARTS_MEDIAN=74997630;END_EVENT_SIZE_STD_DEV=0.0;END_EVENT_SIZE_MEDIAN=1;END_EVENT_SIZE_MEAN=1;END_UNCERTAINTY=1.0;END_EVENT_HEURISTIC=0.0 GT 0/1
This is one of the SV hits: as you have stated in the docs looking at the BP notation, it is a "Deletion like". Could you be more specific how it can be a deletion like event since there is information of 2 chromosomes (CHROM=chr 11 and ALT=chr9 present). Even other events like "both the inversions" and the "duplication like" have similar cases
2) How the actual "Translocations", inter and intra chromosomal translocations, are interpreted by the tool?
3) What is the difference between head-to-head Inversion and tail-to-tail inversion