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<div class="moz-cite-prefix">Hello,<br>
<br>
Finally I'm not going to use VCF format as output.<br>
From original input VFC I need to print into my output Chromosome,
Position, Ref_Allele and Var_Allele columns.<br>
<br>
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 ";".<br>
Is there any way to force VEP to print empty extra parameters?<br>
<br>
ie:<br>
<br>
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=<br>
<br>
Or simply fill print empty extra empty fields with =EMPTY.<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 04/17/13 16:53, Guillermo Marco Puche wrote:<br>
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<blockquote cite="mid:516EB780.2080004@sistemasgenomicos.com"
type="cite">
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<div class="moz-cite-prefix">Again, thank you so much !<br>
<br>
I'm looking further VCFTools, maybe it should be the easiest and
standard way to parse VCF output from VEP.<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 04/17/13 16:50, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX3bPzNJCqmdqrikYc-uvStDzFLYp80o-PVUiP-aFXBAhQ@mail.gmail.com"
type="cite">
<pre wrap="">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
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:guillermo.marco@sistemasgenomicos.com"><guillermo.marco@sistemasgenomicos.com></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:guillermo.marco@sistemasgenomicos.com"><guillermo.marco@sistemasgenomicos.com></a> 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
(<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/variation/vep/vep_script.html#plugins">http://www.ensembl.org/info/docs/variation/vep/vep_script.html#plugins</a>)
explains all of this, but the best way to see how plugins work is to
look at the existing plugins at
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://github.com/ensembl-variation/VEP_plugins">https://github.com/ensembl-variation/VEP_plugins</a>. 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
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:guillermo.marco@sistemasgenomicos.com"><guillermo.marco@sistemasgenomicos.com></a> 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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