[ensembl-dev] VEP error when using --regulatory flag

Siddharth Sethi s.sethi at har.mrc.ac.uk
Fri Apr 19 15:02:13 BST 2013


Hi Will,

Its working brilliantly now.
Thank you very much for this.

Regards,
Sid

-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 19 April 2013 11:56
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP error when using --regulatory flag

Hello again,

Thanks for this very helpful bug report - I've committed a fix for this to CVS.

You should download and re-install the ensembl-variation CVS module or re-run the INSTALL.pl if that's how you set the VEP up.

Regards

Will

On 19 April 2013 10:38, Siddharth Sethi <s.sethi at har.mrc.ac.uk> wrote:
> Hello Will,
>
> I have attached it again.
> Here is a snippet of the file:
>
> 1       55276719        .       A       G       283.01  PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.000;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=1.9998;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.556;QD=17.69;ReadPosRankSum=-0.340;SB=-1.190e+02;VQSLOD=17.4764;culprit=MQ  GT:AD:DP:GQ:PL  0/1:7,8:16:99:313,0,268
> 1       130832845       .       A       G       292.01  PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.825;DP=12;Dels=0.00;FS=3.090;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.239;QD=24.33;ReadPosRankSum=-1.239;SB=-1.340e+02;VQSLOD=18.7196;culprit=HaplotypeScore      GT:AD:DP:GQ:PL  0/1:4,8:12:99:322,0,139
> 1       165036668       .       A       G       274.01  PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.355;DP=15;Dels=0.00;FS=0.000;HaplotypeScore=2.9950;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.530;QD=18.27;ReadPosRankSum=-1.827;SB=-6.601e+01;VQSLOD=4.4589;culprit=ReadPosRankSum     GT:AD:DP:GQ:PL  0/1:6,9:15:99:304,0,218
> 1       162777589       .       T       A       327.01  PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.416;DP=15;Dels=0.00;FS=2.059;HaplotypeScore=1.9982;MLEAC=1;MLEAF=0.500;MQ=58.45;MQ0=0;MQRankSum=-0.177;QD=21.80;ReadPosRankSum=-1.709;SB=-1.160e+02;VQSLOD=3.8575;culprit=ReadPosRankSum     GT:AD:DP:GQ:PL  0/1:6,9:15:99:357,0,212
>
> Thank you,
> Sid
>
> -----Original Message-----
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On
> Behalf Of Will McLaren
> Sent: 19 April 2013 10:30
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] VEP error when using --regulatory flag
>
> Hello Sid,
>
> It seems your attachment hasn't made it through - perhaps you could paste the data into an email if it is small enough?
>
> Thanks
>
> Will McLaren
> Ensembl Variation
>
>
> On 19 April 2013 10:16, Siddharth Sethi <s.sethi at har.mrc.ac.uk> wrote:
>> Hi ,
>>
>>
>>
>> I am using the latest version (v71) and using the VCF format
>> (VCFv4.1) generated from GATK.
>>
>> The script breaks down when I use the -regulatory flag while it runs
>> fine when I remove the flag.
>>
>> Also, it runs fine even with -regulatory for some VCF while it gives
>> error with others, which is strange because all the VCF have been
>> generated from the same pipeline.
>>
>> The script exits with the following error :
>>
>>
>>
>> 2013-04-18 16:28:54 - Read existing cache info
>>
>> 2013-04-18 16:28:54 - Starting...
>>
>> 2013-04-18 16:28:54 - Read 2125 variants into buffer
>>
>> 2013-04-18 16:28:54 - Reading transcript data from cache and/or
>> database
>>
>> [====================================================================
>> = =============================================================]
>> [ 100% ]
>>
>> 2013-04-18 16:30:39 - Retrieved 50462 transcripts (0 mem, 52330
>> cached, 0 DB, 1868 duplicates)
>>
>> 2013-04-18 16:30:39 - Reading regulatory data from cache and/or
>> database
>>
>> [========>
>> ]    [ 7% ]Can't call method "isa" on unblessed reference at
>> EnsemblAPI_71/ensembl-tools/scripts/variant_effect_predictor/Bio/EnsE
>> M BL/Funcgen/DBSQL/BaseFeatureAdaptor.pm
>> line 133, <GEN0> line 2125.
>>
>>
>>
>>
>>
>> This is the command :
>>
>> perl
>> EnsemblAPI_71/ensembl-tools/scripts/variant_effect_predictor/variant_
>> e ffect_predictor.pl -cache -i input.vcf -o VEP_output -species
>> mus_musculus -format vcf --force -sift b -regulatory
>>
>>
>>
>> I have attached a test VCF file which is producing this error.
>>
>>
>>
>> Can you please help me in fixing this error
>>
>> I will appreciate any kind of help.
>>
>>
>>
>> Thank you
>>
>>
>>
>> Sid
>>
>> Bioinformatics
>>
>> MRC Harwell
>>
>> Mammalian Genetics Unit
>>
>> Harwell Science and Innovation Campus Oxfordshire
>>
>> OX11 0RD, UK
>>
>>
>>
>>
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