[ensembl-dev] Variant effect predictor: regulatory information and MATRIX/HIGH_INF_POS

[A. P. Levine]

I have two questions regarding the Variant Effect Predictor (VEP).

1. Regulatory information

When I use the VEP online it gives me the regulatory feature information without a problem. However, when I use the Perl script it does not report this information, e.g.:

Input (VCF format):
18   10304   .       TACCC   TAACCC
18   10333   .       T       C
18   10334   .       T       A
18   10405   .       C       T
18   10411   .       TA      TAA

Output from web version:
Uploaded Variation    Location    Allele    Gene    Feature    Feature type    Consequence    Position in cDNA    Position in CDS    Position in protein    Amino acid change    Codon change    Co-located Variation    Extra
18_10305_ACCC/AACCC    18:10305-10308    -    -    -    -    INTERGENIC    -    -    -    -    -    -    -
18_10305_ACCC/AACCC    18:10305-10308    AACCC    -    ENSR00000667451    RegulatoryFeature    REGULATORY_REGION    -    -    -    -    -    -    -
18_10333_T/C    18:10333    C    -    ENSR00000667451    RegulatoryFeature    REGULATORY_REGION    -    -    -    -    -    -    -
18_10333_T/C    18:10333    -    -    -    -    INTERGENIC    -    -    -    -    -    -    -
18_10334_T/A    18:10334    A    -    ENSR00000667451    RegulatoryFeature    REGULATORY_REGION    -    -    -    -    -    -    -
18_10334_T/A    18:10334    -    -    -    -    INTERGENIC    -    -    -    -    -    -    -
18_10405_C/T    18:10405    -    -    -    -    INTERGENIC    -    -    -    -    -    -    -
18_10405_C/T    18:10405    T    -    ENSR00000667451    RegulatoryFeature    REGULATORY_REGION    -    -    -    -    -    -    -
18_10441_C/T    18:10441    T    -    ENSR00000667451    RegulatoryFeature    REGULATORY_REGION    -    -    -    -    -    rs56928311    -

Output from Perl script (perl variant_effect_predictor.pl -i test -o test.out --sift b --polyphen b --condel b --regulatory --hgvs --gene --hgnc --check_existing):
#Uploaded_variation     Location        Allele  Gene    Feature Feature_type    Consequence     cDNA_position   CDS_position    Protein_position        Amino_acids     Codons  Existing_variation    Extra
18_10305_ACCC/AACCC     18:10305-10308  -       -       -       -       INTERGENIC      -       -       -       -       -       -       -
18_10333_T/C    18:10333        -       -       -       -       INTERGENIC      -       -       -       -       -       -       -
18_10334_T/A    18:10334        -       -       -       -       INTERGENIC      -       -       -       -       -       -       -
18_10405_C/T    18:10405        -       -       -       -       INTERGENIC      -       -       -       -       -       -       -
18_10441_C/T    18:10441        -       -       -       -       INTERGENIC      -       -       -       -       -       rs56928311      -

Any thoughts on why it might not be working would be appreciated.

2. MATRIX/HIGH_INF_POS

The header from running the perl script is as follows:
    ## ENSEMBL VARIANT EFFECT PREDICTOR v2.1
    ## Output produced at 2011-10-05 21:44:03
    ## Connected to homo_sapiens_core_63_37 on ensembldb.ensembl.org
    ## Using API version 63, DB version 63
    ## Extra column keys:
    ## HGNC         : HGNC gene identifier
    ## ENSP         : Ensembl protein identifer
    ## HGVSc        : HGVS coding sequence name
    ## HGVSp        : HGVS protein sequence name
    ## SIFT         : SIFT prediction
    ## PolyPhen     : PolyPhen prediction
    ## Condel       : Condel SIFT/PolyPhen consensus prediction
    ## MATRIX       : The source and identifier of a transcription factor binding profile aligned at this position
    ## HIGH_INF_POS : A flag indicating if the variant falls in a high information position of a transcription factor binding profile

Are MATRIX and HIGH_INF_POS operational?

Thank you,

Adam

Adam P. Levine
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