Keep values from VCF file into Ensembl VEP annotation

Question

[brunobsouzaa]

Hi everyone. Does anyone knows how to keep VCF fields QUAL and FILTER when using tab output format from Ensembl VEP? I could just use bcftools to extract those values into another file them use awk to match POS, REF and ALT values and them print those values into another column from my vep output but, I'm wondering if there's an easier way to do this! My vep script looks like this:

$VEP -i ${i}.vcf --assembly GRCh37 --format vcf -o ${i}.vep --tab --fields "$FIELDS" --sift p --polyphen p --ccds --hgvs --symbol --numbers --regulatory --canonical --protein --biotype --gene_phenotype --af_gnomad --max_af --pubmed --variant_class --hgvs  --fasta $REF --dir $VEP_CACHE --no_stats --use_given_ref --force_overwrite --offline --cache --refseq --flag_pick --fork 20 --verbose --plugin $PLUGINS --custom $CUSTOM

I've searched Ensembl VEP website but found nothing regarding this task.

Appreciate any help. Thanks!

Answer 1

[DareDevil]

The VEP TSV format can only keep in its own specified columns. If you want to maintain the data from your original input, get your output in VCF. It will add the VEP annotation to the INFO column, and keep all the stuff you already have there.

[brunobsouzaa]

Thanks Man... I've wroten a simple awk command for this task! Everything is working fine.

[DareDevil]

it would be great and helpful to others if you share your answer here.

[nihilior]

In case you choose to output a vcf, it may be parsed with SnpSift ExtractFields (https://pcingola.github.io/SnpEff/ss_extractfields/) for the standard vcf fields and VEP Annotation Reporter (https://vatools.readthedocs.io/en/latest/vep_annotation_reporter.html) for the VEP-specific CSQ field