IGV and delly VCF discrepancies

[thedam]

Hi, I've noticed some discrepancies in the delly.vcf output file and what is displayed in IGV.

I've loaded .bam and .vcf to IGV. When I scroll to see the variants I see such picture:

so basically I see BND variant under the postion:
chr1:3074907-3074907

however as you see on the picture, there are no reads. I checked in command line too:
samtools view sample.bam 1:3074900-3074907
(no output)

When I grep the variant in the .vcf file (this is file obtained with: delly/scripts/delly2bnd.py)

1 208267466 BND00008607_1st C ]4:3074906]C 556 PASS PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv1.2.6;END=208267467;CHR2=4;POS2=3074906;PE=0;MAPQ=0;CT=5to3;CIPOS=-30,30;CIEND=-30,30;SRMAPQ=60;INSLEN=0;HOMLEN=29;SR=14;SRQ=0.962963;CONSENSUS=AGATTACTTTCCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCGATGTAATTGACCCCCATTTACAGATGATGCAGCTTTAA;CE=1.95813;CONSBP=41;RDRATIO=1;AC=1;AN=2;MATEID=BND00008607_2nd GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-190.279,0,-165.834:10000:PASS:34793:95869:61076:2:0:0:56:67

4 3074906 BND00008607_2nd G G[1:208267466[ 556 PASS PRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv1.2.6;END=3074907;CHR2=1;POS2=208267466;PE=0;MAPQ=0;CT=3to5;CIPOS=-30,30;CIEND=-30,30;SRMAPQ=60;INSLEN=0;HOMLEN=29;SR=14;SRQ=0.962963;CONSENSUS=AGATTACTTTCCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCGATGTAATTGACCCCCATTTACAGATGATGCAGCTTTAA;CE=1.95813;CONSBP=41;RDRATIO=1;AC=1;AN=2;MATEID=BND00008607_1st GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-190.279,0,-165.834:10000:PASS:34793:95869:61076:2:0:0:56:67

So there is a BND pair in vcf file:
1 208267466 BND00008607_1st
4 3074906 BND00008607_2nd

But IGV shows on the position 1:3074906 variant that should be actually 4:3074906 (and it is there too)

What kind of issue it might be?

[tobiasrausch]

So the delly VCF is correct or is there a bug in the converter script delly2bnd.py?