Using VEP nextflow to add annotation to VCF

Question

[halo22]

Hello,

I am using the nextflow version of VEP as mentioned at https://github.com/Ensembl/ensembl-vep/tree/release/107/nextflow#setup. I have tried running both the tabix indexed VCF version and the non-tabix bgzip version. The workflow stops with a parsing error of the VCF file. Please see the steps mentioned below. I appreciate comments and suggestions.

VCF:

bgzip -c main_vcf > main_vcf.vcf.gz

tabix -p vcf main_vcf.vcf.gz



nextflow -C nf_config/nextflow.config \ 
run workflows/run_vep.nf \
 --vcf main_vcf.vcf.gz \
-profile standard 

N E X T F L O W  ~  version 22.04.5
Launching `workflows/run_vep.nf` [jovial_brattain] DSL2 - revision: 9c873c797d
The specified VCF file has issues in parsing: tbx_index_build failed: main_vcf.vcf.gz 

[colindaven]

Check your vcf especially the header and a few lines for validity - is it the correct format, it sounds like it is not.

Maybe this tool will help or you can find an online tool?

https://github.com/EBIvariation/vcf-validator

[halo22]

I tried running a sample VCF downloaded from http://hgdownload.soe.ucsc.edu/gbdb/hg38/1000Genomes/trio/NA19675_m004_MXL/ the error message remains the same.