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

[Homann, Oliver]

Hello Will,

I am using ver78.  Apologies, but the files yielding this error are quite large (6-30GB) and contain confidential patient information, so I am unable to share them.

Regards,
Oliver

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: Thursday, February 12, 2015 5:52 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP (ver78) TranscriptVariationAllele.pm unitialized value error with --hgvs enabled

Hi Oliver,

Are you able to provide a sample input file that recreates this problem?

There is code in place in the VEP to restore the order as it was in the input file; if you have evidence that this isn't working then it would be useful to see it. The ordering code has been in place since release 75, so if you are using 74 or earlier then obviously this doesn't apply!

Regards

Will McLaren
Ensembl Variation

On 11 February 2015 at 23:38, Homann, Oliver <ohomann at amgen.com<mailto:ohomann at amgen.com>> wrote:
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> [mailto: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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