[ensembl-dev] VEP run with condel, sift and polyphen options
binit treesa
binit.treesa at gmail.com
Mon Oct 15 11:42:35 BST 2012
Will McLaren,
Thanks for spending time on this data.
I rechecked the input data. There are no empty lines.
And I tried the format option in the VEP command as the input is in vcf
format.
Command:
perl variant_effect_predictor.pl -i testinput3.vcf -format vcf -o
outputCondel.txt -sift b -polyphen b -plugin
Condel,/users/tbinit/.vep/Plugins/config/Condel/config,b,2
But still I am getting the same output and showing only 50% completeness in
calculating the consequences.
Here attached the screen shot of VEP run and the output file generated.
Condel scores are pretty same as previous output.
Can you please check this output (condel score) with the one that your VEP
run generated with the the same input.
Thanks
Treesa Binit
>
> ---------- Forwarded message ----------
> From: binit treesa <binit.treesa at gmail.com>
> To: dev at ensembl.org
> Cc: Neeba Dijo <neebasebastian at gmail.com>
> Date: Wed, 10 Oct 2012 16:29:35 +0530
> Subject: VEP run with condel, sift and polyphen options
> Hi,
>
> I have downloaded the VEP version 2.6 and tried to run this script with a
> variant file. It executed succesfully and generated the output file .
> But when I executed this with the options for "sift, polyphen and condel
> plugin", it throws some erros. Eventhough it calculated all the score and
> generated the output file.
>
> And I'm confused on the correctness of these calculated score.
>
> It would be better if you check and comment about the output generated
> here.
>
> Details of the vep.pl run is given below
>
> *Input File :test.txt*
>
> #CHROM_ID START ID REF ALT
> 1 94586536 . C A
> 1 94586536 . C G
>
>
> *Output file : testOutput.txt*
>
> ## ENSEMBL VARIANT EFFECT PREDICTOR v2.6
> ## Output produced at 2012-10-10 06:37:22
> ## Connected to homo_sapiens_core_68_37 on ensembldb.ensembl.org
> ## Using API version 68, DB version 68
> ## Extra column keys:
> ## DISTANCE : Shortest distance from variant to transcript
> ## PolyPhen : PolyPhen prediction
> ## SIFT : SIFT prediction
> ## Condel : Consensus deleteriousness score for an amino acid
> substitution based on SIFT and PolyPhen-2
> #Uploaded_variation Location Allele Gene Feature
> Feature_type Consequence cDNA_position CDS_position
> Protein_position Amino_acids Codons Existing_variation Extra
> 1_94586536_C/A 1:94586536 A ENSG00000198691 ENST00000370225
> Transcript missense_variant,splice_region_variant 153 66 22
> K/N aaG/aaT -
> PolyPhen=possibly_damaging(0.859);Condel=deleterious(0.885);SIFT=tolerated(0.09)
> 1_94586536_C/A 1:94586536 A ENSG00000198691 ENST00000535735
> Transcript missense_variant,splice_region_variant 146 66 22
> K/N aaG/aaT -
> PolyPhen=benign(0.235);Condel=deleterious(0.583);SIFT=tolerated(0.07)
> 1_94586536_C/G 1:94586536 G ENSG00000198691 ENST00000370225
> Transcript missense_variant,splice_region_variant 153 66 22
> K/N aaG/aaC -
> PolyPhen=possibly_damaging(0.859);Condel=deleterious(0.885);SIFT=tolerated(0.09)
> 1_94586536_C/G 1:94586536 G ENSG00000198691 ENST00000535735
> Transcript missense_variant,splice_region_variant 146 66 22
> K/N aaG/aaC -
> PolyPhen=benign(0.235);Condel=deleterious(0.583);SIFT=tolerated(0.07)
>
>
> *Command used*
>
> perl variant_effect_predictor.pl -i test.txt -o testOutput.txt -sift b
> -polyphen b -plugin
> Condel,/users/tbinit/.vep/Plugins/config/Condel/config,b --force
>
> *The status of the processing is shown *
>
> readline() on closed filehandle SIFT at
> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 136.
> readline() on closed filehandle POLYPHEN at
> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 147.
> 2012-10-10 05:50:00 - Loaded plugin: Condel
> 2012-10-10 05:50:02 - Starting...
> 2012-10-10 05:50:02 - Detected format of input file as vcf
> Use of uninitialized value $data[4] in string eq at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 316, <GEN0> line 4.
> Use of uninitialized value $ref in length at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 349, <GEN0> line 4.
> Use of uninitialized value $alt in pattern match (m//) at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 352, <GEN0> line 4.
> Use of uninitialized value $alt in split at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 425, <GEN0> line 4.
> Use of uninitialized value $alt in pattern match (m//) at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 434, <GEN0> line 4.
> Use of uninitialized value $ref in concatenation (.) or string at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 501, <GEN0> line 4.
> Use of uninitialized value $alt in concatenation (.) or string at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 501, <GEN0> line 4.
> Use of uninitialized value $data[2] in string eq at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 501, <GEN0> line 4.
> Use of uninitialized value in pattern match (m//) at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1944, <GEN0> line 4.
> Use of uninitialized value in substitution (s///) at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1944, <GEN0> line 4.
> Use of uninitialized value in string eq at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1945, <GEN0> line 4.
> Use of uninitialized value in pattern match (m//) at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1950, <GEN0> line 4.
> Use of uninitialized value in concatenation (.) or string at
> /depts/pd/refDataManagment/vep_2.6/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1951, <GEN0> line 4.
> WARNING: Start or end -1 coordinate invalid on line 4
> 2012-10-10 05:50:02 - Read 2 variants into buffer
> 2012-10-10 05:50:02 - Skipping 0 non-variant loci
> 2012-10-10 05:50:02 - Reading transcript data from cache and/or database
> [================================================================================================================================]
> [ 100% ]
> 2012-10-10 05:50:06 - Retrieved 9 transcripts (0 mem, 0 cached, 9 DB, 0
> duplicates)
> 2012-10-10 05:50:06 - Analyzing chromosome 1
> 2012-10-10 05:50:06 - Analyzing variants
> [================================================================================================================================]
> [ 100% ]
> 2012-10-10 05:50:08 - Calculating consequences
> [>
> ] [ 0% ]Use of uninitialized value in subtraction (-) at
> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.
> Use of uninitialized value in subtraction (-) at
> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 212, <GEN0> line 4.
> Use of uninitialized value in subtraction (-) at
> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.
> Use of uninitialized value in subtraction (-) at
> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 216, <GEN0> line 4.
> [==============================================================>
> ] [ 50% ]Use of uninitialized value in subtraction (-) at
> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.
> Use of uninitialized value in subtraction (-) at
> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 212, <GEN0> line 4.
> Use of uninitialized value in subtraction (-) at
> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 203, <GEN0> line 4.
> Use of uninitialized value in subtraction (-) at
> /users/tbinit/.vep/Plugins/config/Condel/Condel.pm line 216, <GEN0> line 4.
> [================================================================================================================================]
> [ 100% ]
> 2012-10-10 05:50:11 - Processed 2 total variants (0 vars/sec, 0 vars/sec
> total)
> 2012-10-10 05:50:11 - Finished!
>
>
> Thanks
> Treesa Binit
>
>
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## ENSEMBL VARIANT EFFECT PREDICTOR v2.6
## Output produced at 2012-10-15 05:46:18
## Connected to homo_sapiens_core_68_37 on ensembldb.ensembl.org
## Using API version 68, DB version 68
## Extra column keys:
## DISTANCE : Shortest distance from variant to transcript
## PolyPhen : PolyPhen prediction
## SIFT : SIFT prediction
## Condel : Consensus deleteriousness score for an amino acid substitution based on SIFT and PolyPhen-2
#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra
1_94586536_C/A 1:94586536 A ENSG00000198691 ENST00000370225 Transcript missense_variant,splice_region_variant 153 66 22 K/N aaG/aaT - PolyPhen=possibly_damaging(0.859);Condel=deleterious(0.885);SIFT=tolerated(0.09)
1_94586536_C/A 1:94586536 A ENSG00000198691 ENST00000535735 Transcript missense_variant,splice_region_variant 146 66 22 K/N aaG/aaT - PolyPhen=benign(0.235);Condel=deleterious(0.583);SIFT=tolerated(0.07)
1_94586536_C/G 1:94586536 G ENSG00000198691 ENST00000370225 Transcript missense_variant,splice_region_variant 153 66 22 K/N aaG/aaC - PolyPhen=possibly_damaging(0.859);Condel=deleterious(0.885);SIFT=tolerated(0.09)
1_94586536_C/G 1:94586536 G ENSG00000198691 ENST00000535735 Transcript missense_variant,splice_region_variant 146 66 22 K/N aaG/aaC - PolyPhen=benign(0.235);Condel=deleterious(0.583);SIFT=tolerated(0.07)
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