Thanks for this amazing tool! Wanted to point out that I just switched from Sniffles v2.6.2 to v2.7 and suddenly had some massive duplications that are biologically unrealistic.
Some are as large as chromosomes, here is an example of a 29MB DUP (ripped of the alleles for simplicity), but I have even longer ones.
Scf9YQZ_11_HRSCAF_22 23271923 Sniffles2.INS.dup2F07SA . . 58 PASS PRECISE;SVTYPE=INS;SVLEN=29246330;END=23271924;SUPPORT=6;COVERAGE=15,21,20,17,11;STRAND=+-;STDEV_LEN=0;STDEV_POS=0;VAF=0.500;AC=1 GT:DR:DV:AD:DP:PL:GQ 0/1:17:6:17,6:23:.:12
I saw this is part of a commit of the new version:
372bc60
so I imagine it is intended behavior to some extent, but it is probably good to be aware of it.
It completely crushed my pangenome construction pipeline (vg construct).
Thanks for this amazing tool! Wanted to point out that I just switched from Sniffles v2.6.2 to v2.7 and suddenly had some massive duplications that are biologically unrealistic.
Some are as large as chromosomes, here is an example of a 29MB DUP (ripped of the alleles for simplicity), but I have even longer ones.
Scf9YQZ_11_HRSCAF_22 23271923 Sniffles2.INS.dup2F07SA . . 58 PASS PRECISE;SVTYPE=INS;SVLEN=29246330;END=23271924;SUPPORT=6;COVERAGE=15,21,20,17,11;STRAND=+-;STDEV_LEN=0;STDEV_POS=0;VAF=0.500;AC=1 GT:DR:DV:AD:DP:PL:GQ 0/1:17:6:17,6:23:.:12I saw this is part of a commit of the new version:
372bc60
so I imagine it is intended behavior to some extent, but it is probably good to be aware of it.
It completely crushed my pangenome construction pipeline (vg construct).