VEP error for structural variation VCF input about ensembl-vep HOT 8 CLOSED

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

from ensembl-vep.

Hi @barbarian1803 ,

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

Thank you.

from ensembl-vep.

@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.

from ensembl-vep.

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

from ensembl-vep.

@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

from ensembl-vep.

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

from ensembl-vep.

@likhitha-surapaneni Any update on the solution?

from ensembl-vep.

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

from ensembl-vep.