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

[Will McLaren]

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> 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] *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
> <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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