[ensembl-dev] VEP Extra output information
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Fri Apr 19 07:42:05 BST 2013
Hello,
I'm trying to get the following fields from the VCF input with the
--custom flag.
I want to add the following columns to the VEP output file:
#CHROM POS ID REF ALT QUA
From what I've been reading this is possible to achieve using custom
flag and VCF input, since third column is used as identifier (ID, ie:
rs6054257)
I've been trying with the following command:
*./variant_effect_predictor.pl -i myinput.vcf.gz -format vcf -o
myoutput.vep --cache --everything --maf_1kg --force_overwrite --plugin
Condel,/home/likewise-open/SGNET/gmarco/.vep/Plugins/config/Condel/config,b
--custom myinput.vcf.gz,CHROM,vcf,exact,0 --fields
CHROM,Existing_variation,AFR_MAF,AMR_MAF,ASN_MAF,EUR_MAF,GMAF,Feature,Feature_type,HGVSc,HGVSp,Consequence,Domains,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,Condel,SIFT,Polyphen,Cell_Type,Canonical,CCDS,Intron,Exon*
I got an output like this:
#CHROM Existing_variation AFR_MAF AMR_MAF ASN_MAF EUR_MAF GMAF Feature Feature_type HGVSc HGVSp Consequence Domains MOTIF_NAME MOTIF_POS HIGH_INF_POS Condel SIFT Polyphen Cell_Type Canonical CCDS Intron Exon
1:6500735-6500735 - - - - - - NM_031475.2 Transcript NM_031475.2:c.725C>T NP_113663.2:p.Thr242Ile missense_variant - - - - deleterious(0.765) deleterious(0.03) - - - - - -
1:6501044-6501044 rs2311045 0.28 0.12 0.21 0.13 G:0.1822 ENSR00000074413 RegulatoryFeature - - regulatory_region_variant - - - - - - - - - - - -
1:6501044-6501044 rs2311045 0.28 0.12 0.21 0.13 G:0.1822 CCDS70.1 Transcript CCDS70.1:c.909C>G CCDS70.1:c.909C>G(p.=) synonymous_variant - - - - - - - - - CCDS70.1 - -
Position being show in CHROM column makes no sense to me if it's the key
identifier. If you're using the "exact" configuration in custom flag
with no overlapping why it's an interval shown?
I would like that POS being shown in a second column called POS like in
original VCF and so on with the rest of custom missing fields. Output
format would be:
#CHROM POS ID REF ALT QUA Existing_variation AFR_MAF AMR_MAF ASN_MAF EUR_MAF GMAF Feature Feature_type HGVSc HGVSp Consequence Domains MOTIF_NAME MOTIF_POS HIGH_INF_POS Condel SIFT Polyphen Cell_Type Canonical CCDS Intron Exon
chr1 6501044 rs2311045 0.28 0.12 0.21 0.13 G:0.1822 ENSR00000074413 RegulatoryFeature - - regulatory_region_variant - - - - - - - - - - - -
I've been experiencing errors if I try with the following custom flag:
*--custom myinput.vcf.gz,CHROM,POS,ID,REF,ALT,QUA,vcf,exact,0*
I've no idea how to are more than one custom flag at a time, or not even
if this is possible. What would be the correct way to do this?
Thank you.
Best regards,
Guillermo.
On 04/18/13 13:55, Guillermo Marco Puche wrote:
> Hello,
>
> --fields command is working flawlessly ! I love it. It has saved me so
> much work.
>
> ./variant_effect_predictor.pl -i /home/likewise-open/SGNET/gmarco/VEP_71/in/Oto2_collect_not_annotated.vcf -o /home/likewise-open/SGNET/gmarco/VEP_71/out/output.fields -format vcf --cache --everything --maf_1kg --force_overwrite --fork 2 --plugin Condel,/home/likewise-open/SGNET/gmarco/.vep/Plugins/config/Condel/config,b --fields Existing_variation,AFR_MAF,AMR_MAF,ASN_MAF,EUR_MAF,GMAF,Feature,Feature_type,HGVSc,HGVSp,Consequence,Domains,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,Condel,SIFT,Polyphen,Cell_Type,Canonical,CCDS,Intron,Exon
>
> Now I need to figure out how to create a final output file which is
> the relation of VCF input (Chromosome, Position, Ref_Allele,
> Var_Allele) with the VEP output. To display all variants info for each
> chromosome.
>
> Guillermo.
>
> On 04/18/13 10:40, Will McLaren wrote:
>> Hello,
>>
>> The only way to do this would be to specify each Extra column as a
>> separate column using --fields.
>>
>> Will
>>
>> On 18 April 2013 08:29, Guillermo Marco Puche
>> <guillermo.marco at sistemasgenomicos.com> wrote:
>>> Hello,
>>>
>>> Finally I'm not going to use VCF format as output.
>>> From original input VFC I need to print into my output Chromosome, Position,
>>> Ref_Allele and Var_Allele columns.
>>>
>>> I prefer standard VEP column tabbed file for output, since it's much easier
>>> to parse "Extra" column because all extra parameters are delimited by ";".
>>> Is there any way to force VEP to print empty extra parameters?
>>>
>>> ie:
>>>
>>> 1_6508122_G/C 1:6508122 C ENSESTG00000022320 ENSESTT00000056337
>>> Transcript downstream_gene_variant - - - - - rs11808508
>>> AFR_MAF=;DISTANCE=2305;GMAF=;ASN_MAF=;EUR_MAF=;ENSP=ENSESTP00000056337;CANONICAL=YES;AMR_MAF=
>>>
>>> Or simply fill print empty extra empty fields with =EMPTY.
>>>
>>>
>>> Thank you.
>>>
>>> Best regards,
>>> Guillermo.
>>>
>>> On 04/17/13 16:53, Guillermo Marco Puche wrote:
>>>
>>> Again, thank you so much !
>>>
>>> I'm looking further VCFTools, maybe it should be the easiest and standard
>>> way to parse VCF output from VEP.
>>>
>>> Thank you.
>>>
>>> Best regards,
>>> Guillermo.
>>>
>>> On 04/17/13 16:50, Will McLaren wrote:
>>>
>>> Yes, you can customise the fields used and the order they appear in
>>> with --fields; this applies to both VCF and the normal tab-delimited
>>> output.
>>>
>>> The delimiter is hardcoded I'm afraid, but I'm not sure what you'd
>>> pick if you did decide to change it. ";" and "," are already used by
>>> the VCF spec, and ":" appears in HGVS notations and other fields.
>>>
>>> If you did want to change it, you'd just need to edit lines 1272 and
>>> 1275 of ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm.
>>>
>>> Will
>>>
>>>
>>>
>>> On 17 April 2013 15:32, Guillermo Marco Puche
>>> <guillermo.marco at sistemasgenomicos.com> wrote:
>>>
>>> Hello Will,
>>>
>>>
>>> On 04/17/13 14:46, Will McLaren wrote:
>>>
>>> Hello,
>>>
>>> It's difficult (well, in fact impossible) to provide an example where
>>> every field is populated, since some field types are mutually
>>> exclusive dependent on the feature type overlapped (for example, you
>>> will never see the CELL_TYPE field populated for a variant/transcript
>>> combination).
>>>
>>> If you are interested in this for the purposes of how it looks for a
>>> parser, you really want to be looking at the header line added to the
>>> VCF by the VEP:
>>>
>>> ##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|EXON|INTRON|HGNC|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|CLIN_SIG|CANONICAL|SIFT|PolyPhen|GMAF|ENSP|DOMAINS|CCDS|HGVSc|HGVSp|CELL_TYPE|BLOSUM62|CAROL|Conservation|LinkedVariants|INTERPRO|TSSDistance">
>>>
>>> This lists the fields that are added in order. Using this you should
>>> be able to parse what appears in the body of the file.
>>>
>>> Here's an example using a bunch of plugins and with the "--everything"
>>> flag switched on:
>>>
>>> ##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|EXON|INTRON|HGNC|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|CLIN_SIG|CANONICAL|SIFT|PolyPhen|GMAF|ENSP|DOMAINS|CCDS|HGVSc|HGVSp|CELL_TYPE|BLOSUM62|CAROL|Conservation|LinkedVariants|INTERPRO|TSSDistance">
>>> #CHROM POS ID REF ALT QUAL FILTER INFO
>>> 21 26960070 rs116645811 G A . .
>>>
>>> CSQ=|||||||||||||||||||||||||||||||||||,A|ENSG00000154719|ENST00000352957|Transcript|intron_variant||||||rs116645811||9/9|MRPL39||||||||||A:0.0005|ENSP00000284967||CCDS13573.1|ENST00000352957.4:c.969+1077C>T|||||0.840||ENSP00000284967|,A|ENSG00000154719|ENST00000307301|Transcript|missense_variant|1043|1001|334|T/M|aCg/aTg|rs116645811|10/11||MRPL39|||||||YES|tolerated(0.06)|benign(0.001)|A:0.0005|ENSP00000305682|Low_complexity_(Seg):Seg|CCDS33522.1|ENST00000307301.7:c.1001C>T|ENSP00000305682.7:p.Thr334Met||-1|Neutral(0.940)|0.840||ENSP00000305682|
>>>
>>> I like this. It won't be so hard to parse it.
>>>
>>> I've I'm not wrong I can even choose the field order with "--fields" flag.
>>> Is this only working for regular VEP column tabbed output file? Does it work
>>> with VCF output also?
>>>
>>> The only thing I don't like is that delimiter being "|" character is also
>>> used to fill empty fields. It would be great to change delimiter to another
>>> special character so parsing is much easier.
>>>
>>>
>>> Thank you.
>>>
>>> Best regards,
>>> Guillermo.
>>>
>>> This is from input:
>>>
>>> #CHROM POS ID REF ALT QUAL FILTER INFO
>>> 21 26960070 rs116645811 G A . . .
>>>
>>> using the command line:
>>>
>>> perl variant_effect_predictor.pl -i test.txt -force -database
>>> -everything -vcf -plugin Blosum62 -plugin Carol -plugin Conservation
>>> -plugin LD -plugin ProteinDomains -plugin TSSDistance
>>>
>>> Hope this is a bit clearer!
>>>
>>> Will
>>>
>>> On 17 April 2013 11:25, Guillermo Marco Puche
>>> <guillermo.marco at sistemasgenomicos.com> wrote:
>>>
>>> Hello,
>>>
>>> I'm looking for an example *.vcf output with ALL the "Extra" parameters.
>>> I've generated some with VEP script but i'm missing some extras never being
>>> generated like HGNC.
>>>
>>> A few lines VCF with all values would be enough, since i'm planning to parse
>>> "Extra" column.
>>>
>>> It also would be great if it includes most of the plugins outputs also :)
>>>
>>> Thank you :)
>>>
>>> Best regards,
>>> Guillermo.
>>>
>>>
>>> On 04/16/13 18:00, Guillermo Marco Puche wrote:
>>>
>>> On 04/16/13 14:49, Will McLaren wrote:
>>>
>>> Hi Guillermo,
>>>
>>> There's two distinct ways you can add additional data to the output
>>> from the VEP.
>>>
>>> 1) Custom annotations - here you simply provide the VEP with a
>>> tabix-indexed position-based data file, and the VEP does the work of
>>> finding overlaps with your variant input and the data from the file.
>>>
>>> 2) Plugins - you write the code to add to or manipulate the internal
>>> data structures used by the VEP. In its simplest form, a plugin can be
>>> simply looking up an attribute of some object and adding it to the
>>> output.
>>>
>>> Writing a plugin requires a basic understanding of the Ensembl API,
>>> but getting a basic plugin working requires only a very small amount
>>> of code.
>>>
>>> Since additional data is being obtained from multiple sources, APIs, files,
>>> etc.. I guess plugins are the only way to go for me.
>>>
>>> The documentation
>>> (http://www.ensembl.org/info/docs/variation/vep/vep_script.html#plugins)
>>> explains all of this, but the best way to see how plugins work is to
>>> look at the existing plugins at
>>> https://github.com/ensembl-variation/VEP_plugins. I'd suggest looking
>>> at Conservation.pm and ProteinSeqs.pm as some relatively simple
>>> examples of retrieving additional data from the API.
>>>
>>> Where are packages like package Conservation; comming from?
>>>
>>> You should note that using VCF output you will see repeated elements
>>> in the INFO field added, since the plugin gets run once for every
>>> variant/transcript overlap; all data appear under the CSQ field in the
>>> INFO column. Currently there is no way for the VEP via plugins to add
>>> separate INFO fields, however this is something we are looking into,
>>> and in fact would be relatively easy to "hack" in for someone
>>> determined enough (see subroutine vf_list_to_cons in
>>> Bio::EnsEMBL::Variation::Utils::VEP).
>>>
>>> I'll look further into this tomorrow since I've to go now.
>>>
>>> A workaround could be simply generating a temp file with extra columns and
>>> in the end merge original VCF from VEP script with the output from plugins
>>> for additional columns.
>>>
>>> Maybe I missunderstood you. Correct me if i'm wrong please.
>>>
>>> Hope this helps, and feel free to ask further questions!
>>>
>>> Will McLaren
>>> Ensembl Variation
>>>
>>> Thank you so much.
>>>
>>> Best regards,
>>> Guillermo.
>>>
>>> On 16 April 2013 12:58, Guillermo Marco Puche
>>> <guillermo.marco at sistemasgenomicos.com> wrote:
>>>
>>> Hello,
>>>
>>> I'm in need to develop some extra features for VEP.
>>>
>>> My input files are in VCF format and also my output.
>>>
>>> But I want to add several additional columns for extra data at the VCF out.
>>>
>>> For example,AA conservation score, Biobase description, Biobase link, MAF
>>> populations, Flanking sequence, Gene description, InterPro_ID and more..
>>>
>>> I've been reading the documents and I'm a bit confused about "Custom
>>> annotations".
>>> I think since the data I want is extra on the output and not in the input,
>>> what I should do is develop several Plugins to obtain all the values I need.
>>>
>>> I think most of them can be obtained through the Ensembl API even if I'm new
>>> to this. Other will require more hard coding.
>>>
>>> I hope someone can clarify me a bit on this matter.
>>>
>>> Thank you.
>>>
>>> Best regards,
>>> Guillermo.
>>>
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