Hi,

I'm currently running VEP (local mode) on human data using hs1 genome with a GTF file from refseq using the following command :

perl vep --refseq -i my_file.vcf -o my_file_VEP.txt --gtf hs1.ncbiRefSeq.gtf_sorted.gtf.gz --fasta hs1.fa

I have the following warning message for all genes when I run the command (here just 1 line example) :

 WARNING: Parent entries with the following IDs were not found or skipped due to invalid types: TRPC5OS, TRPC5, RTL4, ALG13

I'm quite sure it concern every genes because I obtain only intergenic_variant in the my_file_VEP.txt (~ 5000 lines of variants) .

Any idea why I have this kind of results ?

In this documentation page I read that in ensembl GTF file there is a line describing gene that doesn't exist in refseq GTF file :

1    Ensembl gene        1000  5000  . + . ID=gene1;Name=GENE1

Is it the reason ?

Best,