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

Fri Apr 19 10:38:45 BST 2013

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/EnsEM
> 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
>
>
>
>
> This email may have a PROTECTIVE MARKING, for an explanation please see:
> http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/ind
> ex.htm
>
>
>
> This email may have a PROTECTIVE MARKING, for an explanation please see:
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>
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