How can I revert back the Ensembl vep annotated positions to vcf positions?

Question

[DareDevil]

Sample VCF positions:

CHROM   POS     ID  REF  ALT
chr1    939570   .  T   TCCCTGGAGGACC
chr1    3411794  .  T   C
chr1    1043223  .  CCT C
chr1    22511093 .  CTT CT
chr1    24454031 .  CT  CTT

VEP annotted positions

Positions            Allele
1:939570-939570      CCCTGGAGGACC
1:3411794-3411794        C
1:1043223-1043225        -
1:22511093-22511095      -
1:22511093-22511095      T
1:24454031-24454032      -
1:24454031-24454032      TT

I wanted to revert back VEP positions to VCF positions to remap certain parameters in the VCF file.

Any help appreciated!!!

[finswimmer]

Hello,

can you please describe what your goal is? The Position in the vcf file describes the starting position of the variant, the VEP Position describes the start and end position of the variant. If you transfer this range into your vcf, this is no valid vcf anymore.

fin swimmer

Answer 1

[Emily]

Just get your output in VCF. If using the offline tool, use --vcf. If using the online tool, use the Export options. The VEP annotation will appear as CSQ in the INFO field. If offline, it will also keep all the other stuff from your original VCF.