<div dir="ltr">Hello again,<div><br></div><div>I've fixed a bug that prevented UpDownDistance functioning correctly - it hadn't been tested with larger distances such as you specified which broke some assumptions in the core VEP code.</div>
<div>You will need to update your ensembl-variation module or re-run the VEP INSTALL.pl script to pick up the new API code.</div><div><br></div><div>As far as the other plugins go, I think you are misunderstanding how some of them work:</div>
<div><br></div><div>TSSDistance - this gives the distance between a variant and the annotated transcript start site. If a variant is annotated as intergenic, there is no transcript to give the distance to! Changing the code to force it to assess intergenic variants will of course break here. Of course if you alter the up/down-stream distance using UpDownStream such that this then finds a transcript in range, the plugin will then work as expected without modification. It seems to me that you are expecting that this plugin will find the shortest distance to _any_ transcript start site, which is not the intended purpose of the code.</div>
<div><br></div><div>Condel & dbNSFP - these two plugins work exclusively on missense AKA non-synonymous SNVs (hence the NS in the name dbNSFP). While dbNSFP carries scores for CADD, and CADD gives scores for any genomic position, the CADD scores in dbNSFP are only for missense variants.</div>
<div><br></div><div>The feature_types() subroutine should be used when writing your own plugin to determine which kind of variant/feature combinations are considered by the plugin, since the run() sub is executed once for each variant/feature overlap found by the core VEP code. Modifying existing plugins like this should be done only if you are confident that the modification achieves what you intend.</div>
<div><br></div><div>Hope that all helps</div><div><br></div><div>Will</div><div class="gmail_extra"><br><br><div class="gmail_quote">On 7 May 2014 17:59, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Thanks Will.</div><div><br></div><div>I am working with non-coding and intergenic variants and wanted to run VEP with the following plugins:</div>
<div><br></div><div><div>--plugin UpDownDistance,100000 \</div>
<div>--plugin TSSDistance \</div><div>--plugin Condel,/media/sf_D_DRIVE/Projects/Databases/ensembl/Plugins/Condel/config,b \</div><div>--plugin CADD,/media/sf_D_DRIVE/Projects/Databases/CADD/v1.0/1000G.tsv.gz \</div><div>
--plugin Gwava,tss,/media/sf_D_DRIVE/Projects/Databases/gwava/gwava_scores.bed.gz \</div><div>--plugin Conservation,GERP_CONSERVATION_SCORE,mammals \</div><div>--plugin dbNSFP,/media/sf/data/dbNSFP/dbNSFP2.4.gz,GERP++_NR,GERP++_RS,LRT_score,LRT_pred,MutationTaster_score,MutationTaster_pred,MutationAssessor_score,MutationAssessor_pred,FATHMM_score,FATHMM_pred,RadialSVM_score,RadialSVM_pred,LR_score,LR_pred,Reliability_index,SiPhy_29way_logOdds,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,SIFT_score,SIFT_pred,CADD_raw,CADD_phred</div>
</div><div><br></div><div><br></div><div>As shown in the output below, apart from CADD.pm and Gwava.pm, no scores are returned for the others. dbNSFP.pm should get at least CADD scores because these exist. As recommended I tried using:</div>
<div><br></div><div><div>sub feature_types {</div><div> return ['Feature', 'Intergenic'];</div><div>}</div><div><br></div><div>or</div><div><br></div><div>sub feature_types {</div><div> return ['Transcript', 'Intergenic'];</div>
<div>}</div></div><div><br></div><div>in dbNFSP.pm but does not help. When I tried that in TSSDistance.pm I get this error:</div><div><br></div>Plugin 'TSSDistance' went wrong: Can't locate object method "transcript" via package "Bio::EnsEMBL::Variation::IntergenicVariationAllele" at /media/sf_D_DRIVE/Projects/Databases/ensembl/Plugins//TSSDistance.pm line 56.<br>
<div><br></div><div>For UpDownDistance.pm, it does not seem to work as for instance <span style="font-family:arial,sans-serif">rs140931361 is </span>58298 bp from ENSG00000198822 but this is gene is not returned.</div><div>
<br></div><div><br></div><div>OUTPUT:</div><div><br></div><div><table border="0" cellpadding="0" cellspacing="0" width="4038" style="border-collapse:collapse;width:3029pt">
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<td height="20" colspan="4" width="326" style="height:15pt;width:245pt">## ENSEMBL VARIANT EFFECT PREDICTOR v75</td>
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Output produced at 2014-05-07 17:28:44</td>
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Connected to homo_sapiens_core_75_37 on <a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a></td>
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Using cache in /media/sf_D_DRIVE/Projects/Databases/ensembl//homo_sapiens/75</td>
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Using API version 75, DB version 75</td>
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sift version sift5.0.2</td>
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BIOTYPE : Biotype of transcript</td>
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CANONICAL : Indicates if transcript is canonical for this gene</td>
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CELL_TYPE : List of cell types and classifications for regulatory feature</td>
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CLIN_SIG : Clinical significance of variant from dbSNP</td>
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DISTANCE : Shortest distance from variant to transcript</td>
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DOMAINS : The source and identifer of any overlapping protein domains</td>
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<tr height="20" style="height:15pt">
<td height="20" colspan="3" style="height:15pt">##
ENSP : Ensembl protein identifer</td>
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<tr height="20" style="height:15pt">
<td height="20" colspan="3" style="height:15pt">##
EXON : Exon number(s) / total</td>
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<tr height="20" style="height:15pt">
<td height="20" colspan="9" style="height:15pt">##
HIGH_INF_POS : A flag indicating if the variant falls in a high information
position of the TFBP</td>
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<tr height="20" style="height:15pt">
<td height="20" colspan="3" style="height:15pt">##
INTRON : Intron number(s) / total</td>
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</tr>
<tr height="20" style="height:15pt">
<td height="20" colspan="10" style="height:15pt">##
MOTIF_NAME : The source and identifier of a transcription factor binding
profile (TFBP) aligned at this position</td>
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</tr>
<tr height="20" style="height:15pt">
<td height="20" colspan="6" style="height:15pt">##
MOTIF_POS : The relative position of the variation in the aligned TFBP</td>
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<tr height="20" style="height:15pt">
<td height="20" colspan="10" style="height:15pt">##
MOTIF_SCORE_CHANGE : The difference in motif score of the reference and
variant sequences for the TFBP</td>
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<tr height="20" style="height:15pt">
<td height="20" colspan="6" style="height:15pt">##
PUBMED : Pubmed ID(s) of publications that cite existing variant</td>
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<tr height="20" style="height:15pt">
<td height="20" colspan="4" style="height:15pt">##
PolyPhen : PolyPhen prediction and/or score</td>
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<td height="20" colspan="3" style="height:15pt">##
SIFT : SIFT prediction and/or score</td>
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<tr height="20" style="height:15pt">
<td height="20" colspan="3" style="height:15pt">##
SYMBOL : Gene symbol (e.g. HGNC)</td>
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<tr height="20" style="height:15pt">
<td height="20" colspan="4" style="height:15pt">##
SYMBOL_SOURCE : Source of gene symbol</td>
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<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## TSSDistance</td>
<td colspan="5">: Distance from the
transcription start site</td>
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<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## Condel</td>
<td colspan="10">: Consensus
deleteriousness score for an amino acid substitution based on SIFT and
PolyPhen-2</td>
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<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## CADD_RAW</td>
<td colspan="2">: Raw CADD score</td>
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<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## CADD_PHRED</td>
<td colspan="4">: PHRED-like scaled CADD
score</td>
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<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## GWAVA</td>
<td colspan="6">: Genome Wide Annotation
of VAriants score (tss model)</td>
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<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## Conservation</td>
<td colspan="12">: The conservation score
for this site (method_link_type="GERP_CONSERVATION_SCORE",
species_set="mammals")</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
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<td></td>
<td></td>
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<td></td>
<td></td>
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<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## MutationTaster_score</td>
<td colspan="11">: MutationTaster_score
from dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## Polyphen2_HVAR_score</td>
<td colspan="11">: Polyphen2_HVAR_score
from dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## LRT_pred</td>
<td colspan="10">: LRT_pred from dbNSFP
file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
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<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## MutationAssessor_score</td>
<td colspan="11">: MutationAssessor_score
from dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
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<td></td>
<td></td>
<td></td>
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<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## FATHMM_pred</td>
<td colspan="10">: FATHMM_pred from
dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## LR_score</td>
<td colspan="10">: LR_score from dbNSFP
file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
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<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
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<td></td>
<td></td>
<td></td>
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<td></td>
<td></td>
<td></td>
<td></td>
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<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## MutationTaster_pred</td>
<td colspan="11">: MutationTaster_pred
from dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## SiPhy_29way_logOdds</td>
<td colspan="11">: SiPhy_29way_logOdds
from dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## CADD_phred</td>
<td colspan="10">: CADD_phred from dbNSFP
file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
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<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
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<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## Polyphen2_HVAR_pred</td>
<td colspan="11">: Polyphen2_HVAR_pred
from dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## RadialSVM_pred</td>
<td colspan="10">: RadialSVM_pred from
dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## Reliability_index</td>
<td colspan="10">: Reliability_index from
dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## GERP++_NR</td>
<td colspan="10">: GERP++_NR from dbNSFP
file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## MutationAssessor_pred</td>
<td colspan="11">: MutationAssessor_pred
from dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## LRT_score</td>
<td colspan="10">: LRT_score from dbNSFP
file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## CADD_raw</td>
<td colspan="10">: CADD_raw from dbNSFP
file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## LR_pred</td>
<td colspan="9">: LR_pred from dbNSFP
file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## FATHMM_score</td>
<td colspan="10">: FATHMM_score from
dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
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<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## SIFT_score</td>
<td colspan="10">: SIFT_score from dbNSFP
file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
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</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## GERP++_RS</td>
<td colspan="10">: GERP++_RS from dbNSFP
file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
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</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## SIFT_pred</td>
<td colspan="10">: SIFT_pred from dbNSFP
file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
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</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">## RadialSVM_score</td>
<td colspan="10">: RadialSVM_score from
dbNSFP file /media/sf_Psychiatric_Genetics_yo2/data/dbNSFP/dbNSFP2.4.gz</td>
<td></td>
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</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">#Uploaded_variation</td>
<td>Location</td>
<td>Allele</td>
<td>Existing_variation</td>
<td>SYMBOL</td>
<td>SYMBOL_SOURCE</td>
<td>Gene</td>
<td>ENSP</td>
<td>Feature</td>
<td>Feature_type</td>
<td>BIOTYPE</td>
<td>STRAND</td>
<td>CANONICAL</td>
<td>EXON</td>
<td>INTRON</td>
<td>DISTANCE</td>
<td>TSSDistance</td>
<td>Consequence</td>
<td>cDNA_position</td>
<td>CDS_position</td>
<td>Protein_position</td>
<td>Amino_acids</td>
<td>Codons</td>
<td>PolyPhen</td>
<td>SIFT</td>
<td>Condel</td>
<td>CELL_TYPE</td>
<td>SV</td>
<td>PUBMED</td>
<td>CLIN_SIG</td>
<td>HIGH_INF_POS</td>
<td>MOTIF_NAME</td>
<td>MOTIF_POS</td>
<td>MOTIF_SCORE_CHANGE</td>
<td>TSSDistance</td>
<td>CADD_RAW</td>
<td>CADD_PHRED</td>
<td>GWAVA</td>
<td>Conservation</td>
<td>GERP++_NR</td>
<td>GERP++_RS</td>
<td>LRT_score</td>
<td>LRT_pred</td>
<td>MutationTaster_score</td>
<td>MutationTaster_pred</td>
<td>MutationAssessor_score</td>
<td>MutationAssessor_pred</td>
<td>FATHMM_score</td>
<td>FATHMM_pred</td>
<td>RadialSVM_score</td>
<td>RadialSVM_pred</td>
<td>LR_score</td>
<td>LR_pred</td>
<td>Reliability_index</td>
<td>SiPhy_29way_logOdds</td>
<td>Polyphen2_HVAR_score</td>
<td>Polyphen2_HVAR_pred</td>
<td>SIFT_score</td>
<td>SIFT_pred</td>
<td>CADD_raw</td>
<td>CADD_phred</td>
<td>Extra</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">rs13247133</td>
<td>7:86199080</td>
<td>A</td>
<td>rs13247133</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>intergenic_variant</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td align="right">-0.25769</td>
<td align="right">2.762</td>
<td align="right">0.11</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>CADD_RAW=-0.257691;CADD_PHRED=2.762;GWAVA=0.11</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">rs13244782</td>
<td>7:86202665</td>
<td>T</td>
<td>rs13244782</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>intergenic_variant</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td align="right">1.957591</td>
<td align="right">12.5</td>
<td align="right">0.15</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>CADD_RAW=1.957591;CADD_PHRED=12.50;GWAVA=0.15</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">rs12704267</td>
<td>7:86206830</td>
<td>T</td>
<td>rs12704267</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>intergenic_variant</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td align="right">0.111018</td>
<td align="right">4.597</td>
<td align="right">0.16</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>CADD_RAW=0.111018;CADD_PHRED=4.597;GWAVA=0.16</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">rs140931361</td>
<td>7:86214933-86214937</td>
<td>-</td>
<td>rs140931361</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>intergenic_variant</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td align="right">-0.42024</td>
<td align="right">2.04</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>CADD_RAW=-0.420243;CADD_PHRED=2.040</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">rs34536358</td>
<td>7:86222651</td>
<td>G</td>
<td>rs34536358</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>intergenic_variant</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td align="right">-0.31002</td>
<td align="right">2.524</td>
<td align="right">0.18</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>CADD_RAW=-0.310016;CADD_PHRED=2.524;GWAVA=0.18</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">rs36006360</td>
<td>7:86224933</td>
<td>T</td>
<td>rs36006360</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>intergenic_variant</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td align="right">2.513017</td>
<td align="right">14.36</td>
<td align="right">0.36</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>CADD_RAW=2.513017;CADD_PHRED=14.36;GWAVA=0.36</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">rs13244678</td>
<td>7:86232583</td>
<td>T</td>
<td>rs13244678</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>intergenic_variant</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td align="right">-0.52024</td>
<td align="right">1.626</td>
<td align="right">0.05</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>CADD_RAW=-0.520238;CADD_PHRED=1.626;GWAVA=0.05</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">rs12704279</td>
<td>7:86238294</td>
<td>T</td>
<td>rs12704279</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>intergenic_variant</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td align="right">0.454708</td>
<td align="right">6.469</td>
<td align="right">0.16</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>CADD_RAW=0.454708;CADD_PHRED=6.469;GWAVA=0.16</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">rs13228078</td>
<td>7:86240691</td>
<td>C</td>
<td>rs13228078</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>intergenic_variant</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td align="right">0.980262</td>
<td align="right">9.002</td>
<td align="right">0.1</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>CADD_RAW=0.980262;CADD_PHRED=9.002;GWAVA=0.1</td>
</tr>
<tr height="20" style="height:15pt">
<td height="20" style="height:15pt">rs140931361</td>
<td>7:86214933-86214937</td>
<td>-</td>
<td>rs140931361</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>intergenic_variant</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td align="right">-0.42024</td>
<td align="right">2.04</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>-</td>
<td>CADD_RAW=-0.420243;CADD_PHRED=2.040</td>
</tr></tbody></table></div><div class="gmail_extra"><br></div><div class="gmail_extra">Thanks,</div><div class="gmail_extra"><br></div><div class="gmail_extra">G.<br><br><div class="gmail_quote">On 7 May 2014 16:13, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>Correct, the plugin was intended to work with the whole_genome_SNVs.tsv file, which only contains data for SNVs.</div>
<div><br></div><div>I've modified the plugin so that it should be able to cope with indel data files such as you have; please do let me know if you have any problems as I've only sparingly tested it on made-up data!</div>
<div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On 7 May 2014 15:37, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div><div dir="ltr">Hi,<div><br>
</div><div>There seem to be a discrepancy between the CADD score calculated using VEP with the CADD.pm plugin and the tabix direct output:</div>
<div><br></div><div>For example using this 1000G variant:</div>
<div><br></div><div><div>#CHROM<span style="white-space:pre-wrap"> </span>POS<span style="white-space:pre-wrap"> </span>ID<span style="white-space:pre-wrap"> </span>REF<span style="white-space:pre-wrap"> </span>ALT<span style="white-space:pre-wrap"> </span>QUAL<span style="white-space:pre-wrap"> </span>FILTER<span style="white-space:pre-wrap"> </span>INFO</div>
<div>7<span style="white-space:pre-wrap"> </span>86214932<span style="white-space:pre-wrap"> </span>rs140931361<span style="white-space:pre-wrap"> </span>TTACTC<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>.</div>
<div><br></div><div><a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i input.txt --format vcf --plugin CADD,/media/sf_D_DRIVE/Projects/Databases/CADD/v1.0/1000G.tsv.gz<br></div>
<div>does not return any CADD score</div>
<div><br></div><div>whereas </div><div><div>$ tabix -p vcf 1000G.tsv.gz 7:86214932-86214932</div><div>7<span style="white-space:pre-wrap"> </span>86214932<span style="white-space:pre-wrap"> </span>TTACTC<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>-0.420243<span style="white-space:pre-wrap"> </span>2.040</div>
</div><div><br></div><div>This seems to affect indels and not SNVs. I could see in the plugin that there is a rule to ignore indels. Any suggestions please how to safely change that?</div><div><br></div><div>Also, in the plugin, I assume there is a test to ensure the alleles are identical between the input file and the 1000G.tsv.gz file. Is this correct?</div>
<div><br></div><div>Thanks.</div><span><font color="#888888"><div><br></div>-- <br><div dir="ltr">G.</div>
</font></span></div></div>
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<br></blockquote></div><br></div>
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<br></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
</font></span></div></div>
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<br></blockquote></div><br></div></div>