Missing COSMIC ids

[sean-ocall]

Describe the issue

Following from my closed issue: https://github.com/Ensembl/ensembl-vep/issues/1007

I've now been able to achieve annotation of all of the columns I require, but there is still information missing from one column. My Existing_variation column is not reporting cosmic ids. Is there a flag I have missed? or some incompatible flags?

System

• VEP version: 104
• VEP Cache version: 104
• tabix installed 1.3.1

Full VEP command line

vep -i $TSV_NAME -v --dir_cache $PWD --cache --offline --format ensembl --fasta $PWD/Homo_sapiens.GRCh37.dna.primary_assembly.fa --variant_class --sift b --polyphen b --regulatory --total_length --numbers --no_escape --hgvs --hgvsg --shift_hgvs 0 --symbol --ccds --uniprot --protein --canonical --biotype --domains --xref_refseq --check_existing --exclude_null_alleles --af --af_1kg --af_gnomad --tab -o vep_output.tsv

Full error message

No error, but reported annotation is missing cosmic IDs.

Data files (if applicable)

Input: 1 1722003 1722003 G/A + 1_1722003_G_A

output file attached

In addition, a straight call to tabix: tabix $PWD/homo_sapiens/104_GRCh37/1/all_vars.gz 1:1722003-1722003 returns the following:

1   COSV101060785   .   1   1722003 .   COSMIC_MUTATION .   .   .   .   1   .   .   COSMIC::COSM8502737 .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   .
1   rs200569590 .   .   1722003 .   G/A .   .   .   .   .   .   .   .   .   .   .   .   .   .   .   A:1.592e-05 A:0 A:0 A:0.000298  A:0 A:0 A:8.806e-06 A:0 A:0

so the cache seems to contain the data, but I'm not getting it in the output

vep_output_18062021.txt

Many thanks, Sean

[at7]

Hi Sean, you need to remove --exclude_null_alleles from your options. Alleles are not publicly available for variants from HGMD and COSMIC; by default these are included when using --check_existing. And using --exclude_null_alleles will exclude them.

Best wishes, Anja

[sean-ocall]

Thank you!