Unexprected Ensembl-vep results
Hi.
I got a VCF from an individual that shows symptoms of a known disease with known mutations.
I run it with Ensembl-vep, expecting to find some of those mutations in the results, yet, all the consequences in the results are "intergenic-variant".
The command I used was:
--cache --input_file sample.vcf
According to the VEP summary, the annotation source was:
Cache: /.vep/homo_sapiens/106_GRCh38; homo_sapiens_core_106_38 on ensembldb.ensembl.org
Any ideas why I got this results instead of the expected annotations? From your experience, could the Ensembl-vep result be wrong as a result of the command I used (the VCF file is ok)?
Thanks!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Ensembl vep GRCh38 cache version
written by sg197 •
-
Subset VCF to exon region but still get intron_variant annotation
written by tomas4482 •
-
VEP tool
written by Shweta •
-
Using a Docker image with ensembl-vep
written by langziv •
-
Looking for expected mutations in a VCF file
written by langzvi •
-
Vcf2maf error message: Cannot index bgzipped fasta file
written by Winson •
-
Running VEP without --cache
written by nikitavlassenko
-
How can I get other parameters from Ensembl VEP for vcf annotation
written by mittu1602
-
Ensembl VEP 89 Output Format
written by bruce.moran
-
VCF2MAF does not recognize option --cache-version
written by kjnousia •
maybe your VCF is not GRCh38?
How can i know which is it?
Look in the VCF file header to see if there is a record of genome build used.
According to the header, the reference was "human_g1k_v37". I read that it's a version of hg19. If it's so, than the reference I used might be the issue. Now I need to find how to download and use the hg19 instead of hg38. Thanks.
Is Human_G1K_V37.Fasta Hg19?