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I have two questions regarding the Variant Effect Predictor (VEP).<br>
<br>
1. Regulatory information<br>
<br>
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.:<br>
<br>
Input (VCF format):<br>
18 10304 . TACCC TAACCC<br>
18 10333 . T C<br>
18 10334 . T A<br>
18 10405 . C T<br>
18 10411 . TA TAA<br>
<br>
Output from web version:<br>
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<br>
18_10305_ACCC/AACCC 18:10305-10308 - - - - INTERGENIC - - - - - - -<br>
18_10305_ACCC/AACCC 18:10305-10308 AACCC - ENSR00000667451 RegulatoryFeature REGULATORY_REGION - - - - - - -<br>
18_10333_T/C 18:10333 C - ENSR00000667451 RegulatoryFeature REGULATORY_REGION - - - - - - -<br>
18_10333_T/C 18:10333 - - - - INTERGENIC - - - - - - -<br>
18_10334_T/A 18:10334 A - ENSR00000667451 RegulatoryFeature REGULATORY_REGION - - - - - - -<br>
18_10334_T/A 18:10334 - - - - INTERGENIC - - - - - - -<br>
18_10405_C/T 18:10405 - - - - INTERGENIC - - - - - - -<br>
18_10405_C/T 18:10405 T - ENSR00000667451 RegulatoryFeature REGULATORY_REGION - - - - - - -<br>
18_10441_C/T 18:10441 T - ENSR00000667451 RegulatoryFeature REGULATORY_REGION - - - - - rs56928311 -<br>
<br>
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):<br>
#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra<br>
18_10305_ACCC/AACCC 18:10305-10308 - - - - INTERGENIC - - - - - - -<br>
18_10333_T/C 18:10333 - - - - INTERGENIC - - - - - - -<br>
18_10334_T/A 18:10334 - - - - INTERGENIC - - - - - - -<br>
18_10405_C/T 18:10405 - - - - INTERGENIC - - - - - - -<br>
18_10441_C/T 18:10441 - - - - INTERGENIC - - - - - rs56928311 -<br>
<br>
Any thoughts on why it might not be working would be appreciated.<br>
<br>
2. MATRIX/HIGH_INF_POS<br>
<br>
The header from running the perl script is as follows:<br>
## ENSEMBL VARIANT EFFECT PREDICTOR v2.1<br>
## Output produced at 2011-10-05 21:44:03<br>
## Connected to homo_sapiens_core_63_37 on ensembldb.ensembl.org<br>
## Using API version 63, DB version 63<br>
## Extra column keys:<br>
## HGNC : HGNC gene identifier<br>
## ENSP : Ensembl protein identifer<br>
## HGVSc : HGVS coding sequence name<br>
## HGVSp : HGVS protein sequence name<br>
## SIFT : SIFT prediction<br>
## PolyPhen : PolyPhen prediction<br>
## Condel : Condel SIFT/PolyPhen consensus prediction<br>
## MATRIX : The source and identifier of a transcription factor binding profile aligned at this position<br>
## HIGH_INF_POS : A flag indicating if the variant falls in a high information position of a transcription factor binding profile<br>
<br>
Are MATRIX and HIGH_INF_POS operational?<br>
<br>
Thank you,<br>
<br>
Adam<br>
<br>
Adam P. Levine<br>
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