Polyphen & SIFT not available about ensembl-vep HOT 6 CLOSED

Couple of questions:

• why is the script you are running named variant_effect_predictor.pl? As of release/88 it is simply vep
• what is the full command line you are running?
• which cache file (species, version, assembly) did you install?

from ensembl-vep.

Thanks for the quick reply:

1. That was just a remnant error message from the prior version, it does execute using the 'vep' command

2. The command is input into the command line like so:

perl "-X" "/Users/jcook/ensembl-vep/vep" "--format" "vcf" "--vcf" "--offline" "--no_progress" "--canonical" "--check_existing" "--check_ref" "--force_overwrite" "--numbers" "--domains" "--cache" "--hgvs" "--pubmed" "--sift" "b" "--polyphen" "b" "--buffer_size" "5000" "--dir_cache" "/Users/jcook/.vep" "--input_file" "common_and_clinical_20170130_UNKNOWN.vcf" "--output_file" "common_and_clinical_20170130_UNKNOWN.vcf.out.vcf" "--fork" "2"

As well, the same error occurs when just using the sample provided in the documentation:

./vep -i examples/homo_sapiens_GRCh38.vcf --cache --force_overwrite --sift b

3. I used option 46: homo_sapiens_vep_88_GRCh38.tar.gz

from ensembl-vep.

It may be possible your cache is incomplete or did not unpack correctly, possibly due to lack of disk space.

Can you try:

cat /Users/jcook/.vep/homo_sapiens/88_GRCh38/info.txt

You should get the following:

assembly        GRCh38
sift    b
polyphen        b
source_polyphen 2.2.2
source_sift     sift5.2.2
source_genebuild        2014-07
source_gencode  GENCODE 26
source_assembly GRCh38.p10
variation_cols  variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA,ExAC,ExAC_AFR,ExAC_AMR,ExAC_Adj,ExAC_EAS,ExAC_FIN,ExAC_NFE,ExAC_OTH,ExAC_SAS
source_COSMIC   79
source_HGMD-PUBLIC      20164
source_ESP      20141103
source_ClinVar  201701
source_dbSNP    149
source_1000genomes      phase3
source_ESP      V2-SSA137
source_ExAC     0.3
regulatory      1
source_regbuild 16```

from ensembl-vep.

Haha well it seems the cache file never even downloaded now that I looked into that directory -- All that exists currently is the fasta file and its index file. I'll attempt to re-download the cache file and am sure things will cooperate once that is done.

Thanks for the help!

-cookersjs

from ensembl-vep.

As an aside, it seems the extraction process is the issue -- Within the tmp folder the file has been unzipped but not 'un-tarred'

from ensembl-vep.

This extraction process issue has been fixed in release/88.4

from ensembl-vep.