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When annotating CNVs with VEP, I get the following error:
Illegal division by zero at /media/amontalban/Disc1/VEP/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm line 552, <__ANONIO__> line 144.
My input file is a VCF file with the CNVs that looks like this:
chr1 69037 . N <DEL> 10.5 PASS END=71585;SVLEN=2549;EXONS=1;READSEXP=46;READSOBS=0;READSRATIO=0;BF=10.5;SVTYPE=DEL GT 1/1
chr1 1454345 . N <DUP> 10.3 PASS END=1470163;SVLEN=15819;EXONS=9;READSEXP=892;READSOBS=1122;READSRATIO=1.26;BF=10.3;SVTYPE=DUP GT 0/1
chr1 1633748 . N <DEL> 13.4 PASS END=1634654;SVLEN=907;EXONS=4;READSEXP=84;READSOBS=18;READSRATIO=0.214;BF=13.4;SVTYPE=DEL GT 1/1
chr1 1704550 . N <DUP> 11 PASS END=1709133;SVLEN=4584;EXONS=7;READSEXP=427;READSOBS=570;READSRATIO=1.33;BF=11;SVTYPE=DUP GT 0/1
I'm annotating these variants with a custom file coming from dbVar, that looks like this:
1 10000 nssv16889290 N <DUP> . . DBVARID=nssv16889290;SVTYPE=DUP;END=52000;SVLEN=42001;EXPERIMENT=1;SAMPLESET=1;REGIONID=nsv6138160;AC=1453;AF=0.241208;AN=6026
1 10001 nssv14768 T <DUP> . . DBVARID=nssv14768;SVTYPE=DUP;IMPRECISE;END=88143;CIPOS=0,0;CIEND=0,0;SVLEN=78143;EXPERIMENT=1;SAMPLE=NA12155;REGIONID=nsv7879
1 10001 nssv14781 T <DUP> . . DBVARID=nssv14781;SVTYPE=DUP;IMPRECISE;END=82189;CIPOS=0,0;CIEND=0,0;SVLEN=72189;EXPERIMENT=1;SAMPLE=NA18860;REGIONID=nsv7879
1 10001 nssv14784 T <DUP> . . DBVARID=nssv14784;SVTYPE=DUP;IMPRECISE;END=87466;CIPOS=0,0;CIEND=0,0;SVLEN=77466;EXPERIMENT=1;SAMPLE=NA18975;REGIONID=nsv7879
After doing some digging, I have found that the line of the custom VCF file that generates the problem is this:
2 240692045 nssv211104 G <DEL> . . DBVARID=nssv211104;SVTYPE=DEL;END=240692045;SVLEN=-1;EXPERIMENT=1;SAMPLESET=1;LINKS=dbSNP:ss49921710;REGIONID=nsv192526;SEQ=g
As you can see, this is a 1 bp-long deletion at position chr2:240692045.
After digging deeper, I see that the problem may be that, somewhere in the code, VEP adds one to the start position of the variants in the custom file, and when it computes the length of each variant in this file it ends up in 0 (end - start + 1). In the case of the previous line, the values are: 240692045 - 240692046 + 1 = 0. Note that the value 240692046 is the result adding 1 to the start position of the CNV (240692045).
Then, in line 552 of File.pm module, the error comes because it uses the previously calculated length to calculate the overlap of my input variants with the variants in the custom VCF file, hence the division by zero issue.
I am not sure whether this is an expected behaviour, or a problem with my custom annotation file.
Thank you very much for your help.
Additional information
Please fill in the following sections to help us find the source of your issue as quickly as possible.
Thanks for your query!
We have similar problem reported where the VCF parser had a one-by-off error and I think you are getting the same issue. We are planning to fix it in a future Ensembl VEP version. I will investigate further if your issue gets resolved by the fix in VCF parser and let you know the update.
Can you provide me with the full stdout message? And, also, if possible, the specific input variant that is causing the issue. I have not been able to reproduce the issue as of yet and thus cannot check if the fix we are working on solves your issue.
Describe the issue
When annotating CNVs with VEP, I get the following error:
My input file is a VCF file with the CNVs that looks like this:
I'm annotating these variants with a custom file coming from dbVar, that looks like this:
After doing some digging, I have found that the line of the custom VCF file that generates the problem is this:
As you can see, this is a 1 bp-long deletion at position chr2:240692045.
After digging deeper, I see that the problem may be that, somewhere in the code, VEP adds one to the start position of the variants in the custom file, and when it computes the length of each variant in this file it ends up in 0 (end - start + 1). In the case of the previous line, the values are: 240692045 - 240692046 + 1 = 0. Note that the value 240692046 is the result adding 1 to the start position of the CNV (240692045).
Then, in line 552 of File.pm module, the error comes because it uses the previously calculated length to calculate the overlap of my input variants with the variants in the custom VCF file, hence the division by zero issue.
I am not sure whether this is an expected behaviour, or a problem with my custom annotation file.
Thank you very much for your help.
Additional information
Please fill in the following sections to help us find the source of your issue as quickly as possible.
System
Full VEP command line
Full error message
Data files (if applicable)
Not included.
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