Very large deletion #419
Description
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.