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.

[kheemsk]

Hi @likhitha-surapaneni , I am also having a similar issue. Any update on the problem or is there an easy solution?
Thanks!

[duanjingqi]

@likhitha-surapaneni I have the exactly same issue, and VEP109 reported the same error, it did not help at all. Please help me. My test SV vcf.
test.sv.vcf.gz

[likhitha-surapaneni]

Hi @kheemsk and @duanjingqi ,
Sorry to hear that you are facing the same issue and thank you for your patience. We are currently looking into it and will keep you notified once we have an update.

Kind regards,
Likhitha

[duanjingqi]

@likhitha-surapaneni Any update on the solution?

[davmlaw]

As a workaround, you could try using --custom instead of StructuralVariationOverlap, try params like ,type=overlap,overlap_cutoff=80,same_type=1. If you need both ID and coords call it twice. You can do a bit of post-processing and if you need to do some combine the 2 custom annotations and do some filtering

[nuno-agostinho]

Hey @barbarian1803, @kheemsk, and @duanjingqi,

The issue is related with using breakpoint variants while enabling the --regulatory flag. We patched this bug and the fix will be available in the next release (VEP 113).

In the meantime, please consider either:

• Filtering out breakpoint variants when using the --regulatory flag
• Not using --regulatory when analysing breakpoint variants

We understand that the workarounds are sub-optimal at the moment and we are sorry for the inconvenience.

I will now close this ticket, but please feel free to reply here if you want to discuss this further.

Best regards,
Nuno

[ramprasadn]

@nuno-agostinho, could you give us an update on when the next release is expected to be available?

[nakib103]

Hi @ramprasadn, the current estimation for the release date is to be in first half of October.

[ramprasadn]

Thanks for letting us know @nakib103 !