[ensembl-dev] VEP does not like whitespace in VCF input

[Andrew Parton]

Hi João,

Currently, VEP does not support blank lines within VCF files, however this is something that we intend to change in a future release. In the meantime however, you will need to remove blank lines from your input files for VEP to process them correctly.

Kind Regards,
Andrew

> On 12 May 2018, at 12:58, João Eiras <joao.eiras at gmail.com> wrote:
> 
> Hi.
> 
> I've upgraded VEP in my pipeline to version 92, from version 87.
> I have a big test suite (275 vcf files) with many VCF files which test
> my pipeline, and those are artificial files, created manually which
> naturally contain comments and whitespace.
> 
> VEP 92 stop reading the input when it finds a blank line immediately
> after the header :( Meaning, if my VCF headers and variant lines are
> condensed without any whitespace in the middle, VEP will be able to
> annotate my variants, else it stops at the first blank line.
> 
> Example:
> $ perl $vep_dist/vep \
>  -i a.vcf --format vcf \
>  --cache --offline --merged \
>  --species mus_musculus --assembly GRCm38 \
>  --force_overwrite --verbose \
>  --dir $vep_cache \
>  -o a.vcf.txt \
> 
> $ cat a.vcf
> ##fileformat=VCFv4.1
> ##reference=GRCm38
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
> 
> # Substitutions, non synonymous
> # AGA -> AGT (R/s)
> chr1 99772782 . A T 5000 . . .
> 
> $ cat a.vcf.txt
> ## ENSEMBL VARIANT EFFECT PREDICTOR v92.1
> # ...
> #Uploaded_variantion
> 
> ^^^ End of file
> 
> If my input file however looks like the following it does produce output:
> 
> 
> $ cat a.vcf
> ##fileformat=VCFv4.1
> ##reference=GRCm38
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
> # Substitutions, non synonymous
> # AGA -> AGT (R/s)
> chr1 99772782 . A T 5000 . . .
> 
> # CTG -> ATG (L/m)
> chr1 99772783 . C A 5000 . . .
> 
> $ cat a.vcf.txt
> ## ENSEMBL VARIANT EFFECT PREDICTOR v92.1
> # ...
> #Uploaded_variantion
> chr1_99772782_A/T       ...
> chr1_99772783_C/A       ...
> 
> Is this behavior expected ?
> 
> Thank you.
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