[ensembl-dev] VEP Extra output information
Will McLaren
wm2 at ebi.ac.uk
Mon Apr 22 13:34:58 BST 2013
Hello,
The plugin is run once for each combination of variant and overlapped feature.
Let's say your variant overlaps 4 transcripts (they may be splice
variants of the same gene, or 4 different genes, the principal is the
same). In this case, the plugin's "run" method will be executed 4
times for that variant, once for each transcript. The $tva
TranscriptVariationAllele object in each run will have a different
transcript "attached" to it. I'd recommend stepping through how a
plugin works using Perl's debugger - simply add the line:
$DB::single = 1;
somewhere at the start of the run method, then run the vep with perl's -d flag:
perl -d variant_effect_predictor.pl [etc]
I'm not sure, but it seems like you're preloading all of the VCF in
your plugin at the beginning, and then trying to add the info one at a
time. This is not an ideal way to do it, as for large VCF files you
may run in to memory usage issues, and especially using an array you
may not be able to reliably link the lines from your VCF to the lines
of input going into the VEP (a hash keyed on position would be much
better).
A much better way to do it would be to prepare the VCF file with
tabix. The tabix utility can then retrieve just the relevant line from
the VCF on demand (this is very quick, and you can cache data on the
plugin's hash structure between separate executions of the "run"
method).
In the dbNSFP.pm plugin on GitHub, I do something very very similar to
this. First, I get the variation feature object being passed to the
"run" method - this contains the genomic coordinates of the current
variant:
my $vf = $tva->variation_feature;
I then create a string to pass to tabix, which is chr:start-end; this
means tabix will retrieve the lines from your VCF in that range:
my $pos_string = sprintf("%s:%i-%i", $vf->{chr}, $vf->{start}, $vf->{end});
I then run tabix and open the output as a pipe:
open TABIX, sprintf("tabix %s %s |", $self->{file}, $pos_string);
I can then read lines of VCF from the <TABIX> filehandle, parse them,
and finally add the data to the %return hash that gets sent back at
the end of the plugin.
This return hash must contain key/value pairs that will be printed in
the output. For example, lets say I want to add the variant name from
the VCF file I've just parsed:
return {
"VAR_NAME" => $var_name,
}
where $var_name = 'rs123'. Then in the output you would see (normal,
tab-delimited):
VAR_NAME=rs123
appear in the Extra column of your output file. You could add multiple
values for VAR_NAME, but you'd have to write that as a string, for
example:
return {
"VAR_NAME" => join(",", ($var_name1, $var_name2)),
}
which would give you e.g.
VAR_NAME=rs123,rs456
I'm afraid also at this juncture I have to point out that I'm nearing
the limit of support I'm meant to be giving out to one individual.
While we are here to help and will answer any reasonable questions you
have, we have to stop short of doing people's jobs for them! Anything
more than a base level of help might have to be considered as a
collaboration, and this would require communication between our
respective supervisors.
I hope that the documentation on the website and the example code
(which we try to comment as thoroughly as we can) should be enough to
keep you going, and of course I don't want to put you off using and
helping us improve the VEP.
Regards
Will
On 22 April 2013 12:59, Guillermo Marco Puche
<guillermo.marco at sistemasgenomicos.com> wrote:
> Hello,
>
> I'm starting to develop a simple plugin to write the INFO column from VCF
> input into VEP output.
> As far as I've been seen in Git VEP Plugin repo, VEP script will right the
> value returned by the plugin in run function.
>
> Suppose that I've an array of values with the INFO column. Something like
> this:
> my @info_column = ("info_row1","info_row2","info_row3")
>
> An array containing the content of INFO column for each line of VCF input.
> How do I associate each value to the corresponding VEP line output?
> I guess I cannot simply return the array as the result of my plugin.
>
> Is plugin executed for every line by VEP script?
>
>
> Thank you.
>
> Best regards,
> Guillermo.
>
> On 04/22/13 12:07, Guillermo Marco Puche wrote:
>
> Hello,
>
> Me neither. So I've no clue. I hope someone else can help me.
>
> I've also been looking the plugin code you mentioned.
> I don't really see how to extract the columns from input VCF and intersect
> them with VEP output.
>
> Regards,
> Guillermo.
>
> On 04/22/13 12:01, Will McLaren wrote:
>
> Hello,
>
> I haven't used VCFannotate myself, perhaps I was wrong!
>
> I know of other VEP users who have used it though, maybe someone on
> the list will read this email and can give you some help.
>
> Cheers
>
> Will
>
> On 22 April 2013 10:58, Guillermo Marco Puche
> <guillermo.marco at sistemasgenomicos.com> wrote:
>
> Hello Will,
>
> It seems VCFannotate is made for "Intersect the records in the VCF file with
> targets provided in a BED file.".
> How I'm supposed to intersect the output from vep script (VCF or VEP file)
> with my input file VCF?
>
>
> Thank you.
>
> Best regards,
> Guillermo.
>
> On 04/19/13 11:31, Will McLaren wrote:
>
> Hi Guillermo,
>
> The --custom system doesn't quite work like that. Currently it is set
> up to either provide only the ID or the coordinates of any features it
> finds overlapping your variants in the custom file. It can't pull
> particular fields from a VCF in the way you describe here.
>
> To do so, you'd either have to write a plugin to do this (see the
> dbNSFP.pm plugin for an example of doing similar), or use VCFannotate,
> which I believe can do this sort of thing out of the box.
>
> Regards
>
> Will
>
> On 19 April 2013 07:42, Guillermo Marco Puche
> <guillermo.marco at sistemasgenomicos.com> wrote:
>
> 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 &nbs
> p;
> 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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