[svtoolkit-help] Overlapping CNVs?

[Eddie L. <edd...@pa...>]

Hi,

I ran Genome-STRiP on my dataset and in the output genotype vcf files, I
noticed that some of the reported deletions were overlapping. How should I
interpret such overlapping deletions? Would one of the predicted deletion
be better than the others?

For example:
chr1    2583913 DEL_13  C       <DEL>   .       COVERAGE;DEPTH 
CIEND=-44,45;CIPOS=-44,45;END=2629140;GSCOHERENCE=-6.6125886653079;GSCOHFN=-2.2041962217693;GSCOHPVALUE=0.0399;GSCOORDS=2583629,2583912,2629141,2629308;GSDEPTHCALLTHRESHOLD=1.8113119220635596;GSDEPTHNOBSSAMPLES=2;GSDEPTHNTOTALSAMPLES=2;GSDEPTHOBSSAMPLES=0904,0906;GSDEPTHPVALUE=0.0;GSDEPTHRANKSUMPVALUE=0.913914;GSDEPTHRATIO=1.3544900147632686;GSDMAX=45328;GSDMIN=44329;GSDOPT=45140;<rest
of line clipped>
chr1    2583923 DEL_7   A       <DEL>   .       COVERAGE;DEPTH 
CIEND=-59,59;CIPOS=-59,59;END=2621941;GSCOHERENCE=-3.731442108152636;GSCOHFN=-0.7462884216305272;GSCOHPVALUE=0.6772;GSCOORDS=2583656,2583912,2621951,2622152;GSDEPTHCALLTHRESHOLD=1.6648659343192074;GSDEPTHNOBSSAMPLES=3;GSDEPTHNTOTALSAMPLES=3;GSDEPTHOBSSAMPLES=0708,0904,0913;GSDEPTHPVALUE=0.0;GSDEPTHRANKSUMPVALUE=0.8289357;GSDEPTHRATIO=1.2133095867419799;GSDMAX=38138;GSDMIN=37139;GSDOPT=37940;<rest
of line clipped>
chr1    2583951 DEL_9   A       <DEL>   .       COVERAGE;DEPTH 
CIEND=-121,121;CIPOS=-121,121;END=2617214;GSCOHERENCE=-1.3613655977544998;GSCOHFN=-0.6806827988772499;GSCOHPVALUE=0.601;GSCOORDS=2583824,2583939,2617225,2617334;GSDEPTHCALLTHRESHOLD=1.6374681994307405;GSDEPTHNOBSSAMPLES=2;GSDEPTHNTOTALSAMPLES=2;GSDEPTHOBSSAMPLES=0904,0912;GSDEPTHPVALUE=0.0;GSDEPTHRANKSUMPVALUE=0.9686783;GSDEPTHRATIO=1.4466964842117855;GSDMAX=33385;GSDMIN=32386;GSDOPT=33065;<rest
of line clipped>

Cheers,
Eddie