A lot of overlapping SV presented in delly's output

[lovelycatZ]

Hello, Recently I am using DELLY on a batch of WGS data (~30X) from 1000 Genome Project with the command dellt call, but there were many overlapping SV either the same SV type or different SV type, for example:

chr1 789412 DEL00000001 C <DEL> 200 PASS IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.2.6;END=224012415;PE=8;MAPQ=22;CT=3to5;CIPOS=-198,198;CIEND=-198,198 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-12.9785,0,-78.2122:130:PASS:23374:23280476:2684380:17:15:6:0:0 chr1 789469 DEL00000002 CTGGAATGGAATGGAATGGACTCCAATGGAATGTGGTGGGATGGATTCAAATGGAATGGAATGGAATTGAGTGGATTTGAATTGAATGGAATGGAATGGTATGGAATGGAATGGAATGGAATGAAATGGACTAGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATGTACTTGAATTGTATGGAACGGAATTGAATGGACTCGAAAGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATGAACTCCAATGGAATGGAATGGACTCGAATAGAATGGAATGGAATGGAAAGGACTCGAGTGGGATGGAATGGAGTGGAATGGACTCGAATGGGATGGAATGGAATGGAATGGACTCGAATGGAATGGAACCGAAAGGAATGGAACGGAACGGAACGGAACGCAATGGAATCGACCCGAATGGAATGGAATGGAATGGAATGGAATGGAATGCAATGGAATCGAATGGGATGGAATGTATTGGAATGGACTCGAATGGCATGGACAGGAGTGGACCCGAATGAAATGGAATGGAATGGAATGGTCTCGAGTGGAATGGGATGGGATGGGATGGGATGCGATGGGATGGGATGGGATGGGATGGGATGGGATGGGATGGATTTGAATGGAATAGAATGGAA C 34 LowQual PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.2.6;END=790144;PE=0;MAPQ=0;CT=3to5;CIPOS=-21,21;CIEND=-21,21;SRMAPQ=21;INSLEN=0;HOMLEN=27;SR=2;SRQ=0.966216;CONSENSUS=ATGGTATGGAATGCAATGTAATGGACTCGAATGGAACGGAATGGAATGGACAAGAATTGAATTGAATGGACTGGAATGGAATGGAATGGAATGCAATGGAATGCACTCGAACGGATTGGAATGGAATGGACTCGAATAGAATGGAATA;CE=1.842;CONSBP=71 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-25.2818,0,-25.5082:10000:PASS:14509:28917:34250:1:0:0:11:12

or

chr1 1657089 DUP00000028 T <DUP> 507 PASS IMPRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv1.2.6;END=1722512;PE=10;MAPQ=60;CT=5to3;CIPOS=-170,170;CIEND=-170,170 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-40.7775,0,-99.1665:10000:PASS:4193:7171:3706:2:23:10:0:0 chr1 1696852 DUP00000029 T <DUP> 190 PASS IMPRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv1.2.6;END=1749610;PE=7;MAPQ=28;CT=5to3;CIPOS=-61,61;CIEND=-61,61 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-6.97507,0,-144.806:70:PASS:3071:5445:3326:2:33:7:0:0

How can I interpret these result from a same sample, are they all false positive calls?

[tobiasrausch]

The sub-telomeric regions are very repetitive so these SVs are likely not in high-confidence regions of the genome. It could also be that both alleles are non-reference and thus you get overlapping SVs, something we commonly observe for VNTR and STR loci.

[lovelycatZ]

Both of your points are possible in normal case. But I observed there are a lot of overlapping DEL and DUP in the whole sample with large fragments(>10MB). Some DEL and DUP overlap at the same site, and others are very large fragments that cover most of the small CNVs in the results. I think it's implausible because it's impossible for a healthy person to carry so many large CNVs due to their lethal.