[ensembl-dev] VEP predictor 2.5

nathalie nac at sanger.ac.uk
Tue May 15 14:51:26 BST 2012


HI,

I am using VEP predictor 2.5 with my vcf files and  I want to see a vcf 
output with all consequences without the | separator but  with a tab 
separator

This is the command I use:
./variant_effect_predictor.pl -i in  -o out.VEP2.5 -sift=b -polyphen=b 
--check_existing --hgnc --gene --protein --vcf

I would like a mix between the output you get choosing without the vcf 
option and still have GT:AD:DP:GQ:PL   CHROM  POS     ID      REF     
ALT     QUAL    FILTER  from the vcf file

This is my output file:
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as 
predicted by VEP. Format: 
Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_
acids|Codons|Existing_variation|PolyPhen|SIFT|HGNC|ENSP">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  
MKS97
Chr1    5002713 rs6669905       T       C       51.36   PASS    
CSQ=C||||INTERGENIC||||||rs6669905||||  GT:AD:DP:GQ:PL  
0/1:2,3:5:63.59:81,0,64
Chr1    5036174 rs6689050       G       C       31.02   PASS    
CSQ=C||||INTERGENIC||||||||||   GT:AD:DP:GQ:PL  0/1:2,2:4:61.01:61,0,67
Chr1    50162840        rs6689057       C       T       408.03  PASS    
CSQ=T|ENSG00000186094|ENST00000371839|Transcript|INTRONIC||||||rs6689057|||AGBL4|ENSP00000360905,T|ENSG00000186094|ENS
T00000411952|Transcript|INTRONIC||||||rs6689057|||AGBL4|ENSP00000411423,T|ENSG00000186094|ENST00000497451|Transcript|WITHIN_NON_CODING_GENE&INTRONIC||||||rs6689057|||AGBL4|,T|ENSG00000186094
|ENST00000371838|Transcript|INTRONIC||||||rs6689057|||AGBL4|ENSP00000360904,T|ENSG00000186094|ENST00000371836|Transcript|INTRONIC||||||rs6689057|||AGBL4|ENSP00000360902        
GT:AD:DP:GQ:PL
         0/1:11,14:25:99:438,0,353



Without the --vcf option the output is like this
  #Uploaded_variation     Location        Allele  Gene    Feature 
Feature_type    Consequence     cDNA_position   CDS_position    
Protein_position        Amino_acids     Codons  Existing_varia
tion    Extra
rs2480683       1:50661411      T       ENSG00000162374 ENST00000371824 
Transcript      SYNONYMOUS_CODING       944     687     229     P       
ccC/ccT rs2480683       ENSP=ENSP00000360889;H
GNC=ELAVL4
rs2480683       1:50661411      T       ENSG00000162374 ENST00000448907 
Transcript      SYNONYMOUS_CODING       847     696     232     P       
ccC/ccT rs2480683       ENSP=ENSP00000399939;H
GNC=ELAVL4
rs2480683       1:50661411      T       ENSG00000162374 ENST00000371821 
Transcript      SYNONYMOUS_CODING       1017    702     234     P       
ccC/ccT rs2480683       ENSP=ENSP00000360886;H


  I would like to see the vcf (below) with the rest of the file like in 
the example just above
CHROM  POS     ID      REF     ALT     QUAL    FILTER
Chr1    5002713 rs6669905       T       C       51.36   PASS   
GT:AD:DP:GQ:PL  0/1:2,3:5:63.59:81,0,64


is there an option in VEP 2.5 to do this? could you help?
thanks
Nat




More information about the Dev mailing list