[ensembl-dev] VEP run with condel, sift and polyphen options
binit treesa
binit.treesa at gmail.com
Wed Oct 17 07:29:14 BST 2012
Thank you so much Will McLaren !!
I compared output with yours. It shows difference in the condel score. For
previous run, I missed to copy methdist files (
https://github.com/ensembl-variation/VEP_plugins/tree/master/config/Condel/methdist)
in the config folder and this caused the errors.
Now that, the errors are resolved completely. I'm getting the output same
as yours :)
Thank you once again
Binit
On Tue, Oct 16, 2012 at 6:33 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:
> Hello,
>
> I think my output looks the same as yours. Output on STDOUT:
>
> perl variant_effect_predictor.pl -i binit.txt -force -sift b -poly b
> -plugin Condel,[hidden]/Plugins/config/Condel/config,b
> 2012-10-15 12:33:21 - Loaded plugin: Condel
> 2012-10-15 12:33:21 - Starting...
> 2012-10-15 12:33:21 - Detected format of input file as vcf
> 2012-10-15 12:33:21 - Read 2 variants into buffer
> 2012-10-15 12:33:21 - Skipping 0 non-variant loci
> 2012-10-15 12:33:21 - Reading transcript data from cache and/or database
>
> [==========================================================================================================]
> [ 100% ]
> 2012-10-15 12:33:22 - Retrieved 9 transcripts (0 mem, 0 cached, 9 DB,
> 0 duplicates)
> 2012-10-15 12:33:22 - Analyzing chromosome 1
> 2012-10-15 12:33:22 - Analyzing variants
>
> [==========================================================================================================]
> [ 100% ]
> 2012-10-15 12:33:22 - Calculating consequences
>
> [==========================================================================================================]
> [ 100% ]
> 2012-10-15 12:33:22 - Processed 2 total variants (2 vars/sec, 2 vars/sec
> total)
> 2012-10-15 12:33:22 - Finished!
>
> Output in variant_effect_output.txt:
>
> ## ENSEMBL VARIANT EFFECT PREDICTOR v2.6
> ## Output produced at 2012-10-15 12:33:21
> ## Connected to homo_sapiens_core_68_37 on ensembldb.ensembl.org
> ## Using API version 68, DB version 68
> ## Extra column keys:
> ## CELL_TYPE : List of cell types and classifications for regulatory
> feature
> ## 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(0.629);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=neutral(0.343);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(0.629);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=neutral(0.343);SIFT=tolerated(0.07)
>
> Cheers
>
> Will
>
> On 16 October 2012 07:36, binit treesa <binit.treesa at gmail.com> wrote:
> > Thank you for your help.
> >
> > I verified all those things that you suggested. I feel there is no
> problem
> > with config and condel.pm.
> >
> > It would be much thankful, if you send me the output file that you
> > generated.
> >
> >
> > On Mon, Oct 15, 2012 at 5:10 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:
> >>
> >> Hello again,
> >>
> >> I still don't see these errors - perhaps your Condel configuration
> >> file is missing some values?
> >>
> >> Also try updating your Condel.pm and config from the GitHub repository
> >> again.
> >>
> >> Mine looks like:
> >>
> >> > cat ~/.vep/Plugins/config/Condel/config/condel_SP.conf
> >> condel.dir='~/.vep/Plugins/config/Condel/'
> >>
> >>
> >>
> #------------------------------------------------------------------------------
> >> cutoff.HumVar.sift='0.15'
> >> cutoff.HumVar.polyphen='0.28'
> >> cutoff.HUmVar.condel='0.46'
> >>
> >>
> #------------------------------------------------------------------------------
> >> max.HumVar.sift='1'
> >> max.HumVar.polyphen='1'
> >>
> >> On 15 October 2012 11:42, binit treesa <binit.treesa at gmail.com> wrote:
> >> > 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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