[ensembl-dev] errors in with incomplete_terminal_codon_variant

Michael Yourshaw myourshaw at ucla.edu
Wed May 23 20:37:12 BST 2012


With Ensembl version 67, cvs download 2012-05-22 and VEP v 2.5, I’m getting a lot of errors in TranscriptVariationAllele.pm

This is an example of an offending input VCF record:
5       96232565        incomplete_terminal_codon_variant       A       ACC     .       .       .       GT:AB:AD:DP:GQ:PL       0/1:0.88:36,5:41:77.58:78,0,611 1/1:.:0,5:5:12.01:111,12,0

This record has 5 transcripts
	ENST00000513084.1:c.1501_1502insCC
	ENST00000379904.4:c.1366_1367insCC
	ENST00000508077.1:c.488_489insCC
	ENST00000510373.1:c.1501_1502insCC
	ENST00000437043.3:c.1501_1502insCC

All five transcripts cause this error:
	Use of uninitialized value in numeric lt (<) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 980, <GEN9> line 3.

It looks like the error is actually caused by line 986
	elsif( length($self->codon()) < 3 && $hgvs_notation->{type} ne "fs”){
because $self->codon() returns undef when $allele_len=2 and $vf_nt_len=0

Transcript ENST00000508077.1:c.488_489insCC causes two additional errors:
	Use of uninitialized value in substitution (s///) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 997, <GEN9> line 3.
	Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 761, <GEN9> line 3.

For this transcript, $hgvs_notation->{ref} = '' and $hgvs_notation->{alt}  = undef, which seems to cause these errors.



ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

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