[ensembl-dev] VEP (ver78) TranscriptVariationAllele.pm unitialized value error with --hgvs enabled

[Homann, Oliver]

Hello Sarah,

I'm writing to confirm that the issue was solved, and also to report another very minor issue.  I presume VEP is intended to output data in the same order as the records of the VCF input.  This is almost entirely the case for my data, but I find that a set of MT records gets inserted into the middle of the ChrY records near the end of the output.  I've resorted the files to address this inconsistency, but I wanted to bring it to your attention.  If I had to venture a wild guess, perhaps this is due an error with multi-threading logic, in which the final records to return are flushed out of order?

Regards,
Oliver

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Sarah Hunt
Sent: Thursday, February 05, 2015 4:22 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP (ver78) TranscriptVariationAllele.pm unitialized value error with --hgvs enabled


Hi Oliver,

Thanks for the detailed report. This was a similar issue with a stop inserted before the stop not being handled well. It is fixed in branch78 so the consequence of the variant has changed from 'stop_gained' to 'stop_retained'. The HGVS string reflects the synonymous status.

Best wishes,

Sarah

On 03/02/2015 16:52, Homann, Oliver wrote:
Apologies, forgot to clarify that the error occurs in line 1221 of the new version of TranscriptVariationAllele.pm:

   1221   unless( $hgvs_notation->{ref} eq "-"){
   1222       $hgvs_notation->{ref}  = Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq => $hgvs_notation->{ref}, -id => 'ref',  -alphabet => 'protein')) || "";
   1223   }

Regards,
Oliver

From: dev-bounces at ensembl.org<mailto:dev-bounces at ensembl.org> [mailto:dev-bounces at ensembl.org] On Behalf Of Homann, Oliver
Sent: Tuesday, February 03, 2015 8:50 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP (ver78) TranscriptVariationAllele.pm unitialized value error with --hgvs enabled

Hello Sarah,

Your fix worked for all but one of my 'uninitialized value' errors.  Would you mind trying to track down the issue with this remaining problematic entry?

#CHROM             POS        ID            REF         ALT         QUAL    FILTER   INFO      FORMAT              SAMPLENAME
19           42355761             rs374945441       C             CTAGAAA            885.10   .               AC=1;AF=5.556e-03;AN=180;BaseQRankSum=-1.922e+00;DB;DP=2670;FS=2.561;GQ_MEAN=75.28;GQ_STDDEV=91.16;InbreedingCoeff=-0.0056;MLEAC=1;MLEAF=5.556e-03;MQ=60.00;MQ0=0;MQRankSum=-2.160e-01;NCC=0;QD=9.83;ReadPosRankSum=0.353;SOR=0.669               GT:AD:DP:GQ:PL              0/0:17,0:17:34:0,34,505

Thanks,
Oliver




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