VEP custom annotation didn't add INFO field

Question

[MatthewP]

Hello, my vep and cache file is 102 release. I tried to add dbSNP as custom annotation. Here is one sample for test command.

./vep --species homo_sapiens --force_overwrite --cache --dir_cache /opt/vep/.vep/ \
--offline --vcf --stats_file  /opt/vep/.vep/test.html -i /opt/vep/.vep/test.vcf -o /opt/vep/.vep/test.vep.vcf \
--custom /opt/vep/.vep/GCF_000001405.38_GENCODEchrName.vcf.gz,dbSNP,vcf,,,COMMON

I think VEP should add dbSNP and dbSNP_COMMON to INFO field of VCF output. And yes I can see header of this 2 key.

##INFO=<ID=dbSNP,Number=.,Type=String,Description="/opt/vep/.vep/GCF_000001405.38_GENCODEchrName.vcf.gz (overlap)">
##INFO=<ID=dbSNP_COMMON,Number=.,Type=String,Description="COMMON field from /opt/vep/.vep/GCF_000001405.38_GENCODEchrName.vcf.gz">

But the problem is I can't find any dbSNP and dbSNP_COMMON in variant records' INFO field, instead, VEP append this information to CSQ which is default key of VEP annotation.

CSQ=T|intron_variant|MODIFIER|PLCH2|ENSG00000149527|Transcript|ENST00000609981|protein_coding||2/3||||||||||1|cds_end_NF|HGNC|HGNC:29037||rs539400863|cds_end_NF|HGNC|HGNC:29037||rs539400863|

Here is an example use --custom appends "rs539400863" to CSQ, what I expect is "dbSNP=rs539400863"

Answer 1

[Emily]

This is expected behaviour, as shown in this ClinVar example in the documentation. The data is added to the CSQ section of INFO, defined in the headers.