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DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
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How can I interpret germline CNVs? (Updated) #368

Closed removedraft closed 5 months ago

removedraft commented 5 months ago

Among these germline CNVs, what are duplications and what are deletions? How can I find those with copy number 1, 3, 4, etc?


chr20   1408501 CNV00000448 N   <CNV>   10012   PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=1410171;CIPOS=-4,4;CIEND=-4,4;MP=0.83433 GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:0:0,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2:10012:PASS:0:0.025
chr20   1580444 CNV00000449 N   <CNV>   10012   PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=1613490;CIPOS=-67,67;CIEND=-67,67;MP=0.51982 GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:0:0,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2:10012:PASS:0.00472999:0.025
chr20   1913903 CNV00000450 N   <CNV>   485 PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=1915500;CIPOS=-50,50;CIEND=-49,51;MP=1   GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:0:0,-11.1221,-48.4115,-111.868,-201.492,-317.284,-1000.42,-1000.42,-1000.42,-1000.42:111:PASS:0.074964:0.128829
chr20   14211511    CNV00000451 N   <CNV>   47  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=14212517;CIPOS=-381,59;CIEND=-49,51;MP=1 GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:1:-4.29429,0,-4.69648,-18.3837,-41.0617,-72.7305,-113.39,-163.04,-221.681,-289.313:43:PASS:0.977633:0.219783
chr20   16098360    CNV00000452 N   <CNV>   35  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=16104725;CIPOS=-95,95;CIEND=-95,95;MP=0.773049   GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:1:-4.32061,0,-3.54196,-14.9465,-34.2136,-61.3433,-96.3355,-139.19,-189.908,-248.488:35:PASS:1.04952:0.235023
chr20   16779804    CNV00000453 N   <CNV>   65  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=16788637;CIPOS=-95,95;CIEND=-95,95;MP=0.703905   GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:1:-3.85051,0,-6.36806,-22.9547,-49.7599,-86.7836,-134.026,-191.487,-259.166,-1000.21:38:PASS:0.876815:0.206157
chr20   24430775    CNV00000454 N   <CNV>   60  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=24432372;CIPOS=-50,50;CIEND=-49,51;MP=1  GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:0:0,-1.10482,-5.90744,-14.4079,-26.6061,-42.5022,-62.096,-85.3877,-112.377,-143.064:11:LowQual:0.201224:0.342705
chr20   25468243    CNV00000455 N   <CNV>   20  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=25469640;CIPOS=-50,50;CIEND=-49,51;MP=1  GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:0:0,-0.00576016,-1.80266,-5.3907,-10.7699,-17.9402,-26.9017,-37.6543,-50.198,-64.5329:0:LowQual:0.496784:0.492411
chr20   26316951    CNV00000456 N   <CNV>   10012   PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=26322074;CIPOS=-50,50;CIEND=-50,50;MP=0.600976   GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:0:0,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2,-1001.2:10012:PASS:0:0.025
chr20   29122836    CNV00000457 N   <CNV>   21  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=29124920;CIPOS=-423,16;CIEND=-49,51;MP=0.510547  GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:12:-2.95375,-2.44411,-1.97984,-1.56092,-1.18737,-0.859174,-0.57634,-0.338866,-0.146753,0:1:LowQual:11.7353:3.09424
chr20   29328522    CNV00000458 N   <CNV>   29  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=29333796;CIPOS=-50,50;CIEND=-49,51;MP=0.208302   GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:10:-4.45009,-3.59151,-2.82396,-2.14744,-1.56195,-1.06749,-0.664072,-0.351683,-0.130325,0:1:LowQual:9.93163:2.18421
chr20   29333799    CNV00000459 N   <CNV>   27  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=29334884;CIPOS=-50,50;CIEND=-37,1287;MP=1    GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:6:-5.87915,-4.13659,-2.69911,-1.56671,-0.739395,-0.217157,0,-0.0879238,-0.480928,-1.17901:1:LowQual:6.2118:1.19312
chr20   29693673    CNV00000460 N   <CNV>   71  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=29695820;CIPOS=-50,50;CIEND=-99,101;MP=1 GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:1:-3.68193,0,-6.95166,-24.5369,-52.7557,-91.6081,-141.094,-201.214,-271.967,-1000.17:37:PASS:0.846255:0.202093
chr20   29852067    CNV00000461 N   <CNV>   24  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=29853164;CIPOS=-50,50;CIEND=-49,51;MP=1  GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:4:-9.31344,-5.32213,-2.43945,-0.66541,0,-0.443222,-1.99508,-4.65557,-8.42469,-13.3024:4:LowQual:4.10021:0.62589
chr20   30822713    CNV00000462 N   <CNV>   24  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=30837563;CIPOS=-50,50;CIEND=-664,664;MP=0.254915 GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:6:-5.62115,-3.88771,-2.4729,-1.37673,-0.599187,-0.140277,0,-0.178356,-0.675345,-1.49097:1:LowQual:5.94025:1.16747
chr20   30940232    CNV00000463 N   <CNV>   122 PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=30949960;CIPOS=-100,100;CIEND=-27,1035;MP=0.300822   GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:6:-29.5464,-19.8094,-11.9975,-6.11056,-2.14868,-0.111822,0,-1.81321,-5.55145,-11.2147:1:LowQual:5.55809:0.474978
chr20   30966734    CNV00000464 N   <CNV>   21  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=30977758;CIPOS=-50,50;CIEND=-199,201;MP=0.4308   GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:1:-4.57231,0,-1.9169,-10.323,-25.2183,-46.6028,-74.4765,-108.839,-149.692,-197.033:20:PASS:1.2046:0.2587
chr20   31167030    CNV00000465 N   <CNV>   353 PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=31245463;CIPOS=-108158,40;CIEND=-199,201;MP=0.224887 GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:1:-43.1751,0,-35.2232,-148.845,-1000.63,-1000.63,-1000.63,-1000.63,-1000.63,-1000.63:352:PASS:1.05071:0.0744284
chr20   33709673    CNV00000466 N   <CNV>   34  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=33710770;CIPOS=-50,50;CIEND=-49,51;MP=1  GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:0:0,-0.303806,-3.19503,-8.67369,-16.7398,-27.3933,-40.6342,-56.4625,-74.8783,-95.8815:3:LowQual:0.382583:0.409693
chr20   47812192    CNV00000467 N   <CNV>   15  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=47814339;CIPOS=-100,100;CIEND=-49,51;MP=1    GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:1:-2.67607,0,-1.45033,-7.02706,-16.7302,-30.5597,-48.5156,-70.598,-96.8067,-127.142:14:LowQual:1.14852:0.324419
chr20   57525430    CNV00000468 N   <CNV>   130 PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=57527068;CIPOS=-433,23;CIEND=-49,51;MP=0.77561   GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:0:0,-2.57808,-12.9456,-31.1026,-57.049,-90.7849,-132.31,-181.625,-238.729,-303.623:26:PASS:0.169029:0.236123
chr20   61272618    CNV00000469 N   <CNV>   26  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=61276015;CIPOS=-50,50;CIEND=-49,51;MP=1  GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:0:0,-0.399916,-2.53943,-6.41855,-12.0373,-19.3956,-28.4935,-39.331,-51.9082,-66.2249:4:LowQual:0.27011:0.499652
chr20   62335175    CNV00000470 N   <CNV>   19  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=62336272;CIPOS=-50,50;CIEND=-49,51;MP=1  GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:0:0,-0.0209216,-1.71798,-5.09116,-10.1405,-16.8659,-25.2675,-35.3452,-47.0991,-60.5291:0:LowQual:0.487518:0.509024
chr20   64016622    CNV00000471 N   <CNV>   17  PASS    IMPRECISE;SVTYPE=CNV;SVMETHOD=EMBL.DELLYv0.9.1;END=64018099;CIPOS=-50,50;CIEND=-49,51;MP=0.74307    GT:CN:CNL:GQ:FT:RDCN:RDSD   ./.:1:-2.44255,0,-1.71061,-7.57439,-17.5913,-31.7614,-50.0847,-72.5611,-99.1907,-129.973:17:PASS:1.08812:0.323372
tobiasrausch commented 5 months ago

FORMAT/CN is the estimated copy-number (RDCN as a float)