VEP error for structural variation VCF input

[barbarian1803]

Describe the issue

When annotating an SV, VEP throw error.

System

• VEP version: docker 112.0
• VEP Cache version: 112

Full error message

Can't locate object method "cdna_coords" via package "Bio::EnsEMBL::Variation::StructuralVariationOverlap" at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 673, line 3509.

I a not sure which part of the VCF file cause this. Maybe you can help me to narrow down the cause.

[likhitha-surapaneni]

Hi @barbarian1803 ,

Sorry to hear that you are facing issues. Can you please provide us with an input file?

Thank you.

[barbarian1803]

@likhitha-surapaneni Hi, I have narrow down the VCF file that throw this error. I have run this in VEP 109 and it works fine. Attached is the file. test.vcf.gz

The problematic line is:

chr21 46184504 MantaBND:524924:1:2:0:0:0:0 A ]chr21:46184710]TACTCAGGA 159 PASS SVTYPE=BND;SVINSSEQ=TACTCAGG;SVINSLEN=8;BND_DEPTH=356;OriginalId=chr21&46184504&A&]chr21:46184710]TACTCAGGA&665;MATE_BND_DEPTH=341;MATEID=MantaBND:524924:1:2:0:0:0:1;SVOAI=0 GT:FT:GQ:PL:PR:SR:DQ:DN 0/1:PASS:139:189,0,811:15,0:57,13:0:. 0/1:PASS:20:70,0,999:27,0:79,16:.:. 0/0:HomRef:224:0,174,999:18,0:101,14:.:.

chr21 46184710 MantaBND:524924:1:2:0:0:0:1 G GTACTCAGG[chr21:46184504[ 159 PASS SVTYPE=BND;SVINSSEQ=TACTCAGG;SVINSLEN=8;BND_DEPTH=341;OriginalId=chr21&46184710&G&GTACTCAGG[chr21:46184504[&666;MATE_BND_DEPTH=356;MATEID=MantaBND:524924:1:2:0:0:0:0;SVOAI=0 GT:FT:GQ:PL:PR:SR:DQ:DN 0/1:PASS:139:189,0,811:15,0:57,13:0:. 0/1:PASS:20:70,0,999:27,0:79,16:.:. 0/0:HomRef:224:0,174,999:18,0:101,14:.:.

Running in VEP browser also produce the same error.