I'm running DELLY to find SVs in some human samples and upon analyzing the DELLY output (vcf file) I found, what seems to be, a huge deletion...
So, the VCF line I'm talking about is the following:
NC_000001.11 16548095 DEL00000448 C <DEL> 150 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.7.2;END=234776440;PE=0;MAPQ=0;CT=3to5;CIPOS=-1,1;CIEND=-1,1;SRMAPQ=30;INSLEN=0;HOMLEN=0;SR=5;SRQ=0.948601;CONSENSUS=ATACAAACCTGTACTTTCTAC.......;CE=1.99536;CONSBP=968 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-303.122,0,-262.92:10000:PASS:590564299:1420489915:686296029:2:0:0:50:61
So, if I'm interpreting this correctly, the length of this deletion is 234776440 (i.e. the END tag) minus 16548095 (the POS field). Which results in >200 Mbp!! What am I missing? Because I find it hard to believe that such a huge deletion is real...
Just to clarify, I read Tobias's comment on another issue that SVLEN is not reported for deletions (even though I don't quite understand the reason) and that's why I'm calculating the length using the END tag from the INFO field.
I'm running DELLY to find SVs in some human samples and upon analyzing the DELLY output (vcf file) I found, what seems to be, a huge deletion...
So, the VCF line I'm talking about is the following:
So, if I'm interpreting this correctly, the length of this deletion is
234776440(i.e. theENDtag) minus16548095(thePOSfield). Which results in >200 Mbp!! What am I missing? Because I find it hard to believe that such a huge deletion is real...Just to clarify, I read Tobias's comment on another issue that
SVLENis not reported for deletions (even though I don't quite understand the reason) and that's why I'm calculating the length using theENDtag from theINFOfield.