[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
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