WARNING: unknown severity

[davemcg]

WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000372426|1/8|||1/229|protein_coding||||||ENST00000372426.1:c.1dup|ENSP00000361503.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000372426|1/8|||1/229|protein_coding||||||ENST00000372426.1:c.1dup|ENSP00000361503.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000583037|2/8|||1/204|protein_coding||||||ENST00000583037.1:c.1dup|ENSP00000461969.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000583037|2/8|||1/204|protein_coding||||||ENST00000583037.1:c.1dup|ENSP00000461969.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000583037|2/8|||1/204|protein_coding||||||ENST00000583037.1:c.1dup|ENSP00000461969.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000583037|2/8|||1/204|protein_coding||||||ENST00000583037.1:c.1dup|ENSP00000461969.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000583037|2/8|||1/204|protein_coding||||||ENST00000583037.1:c.1dup|ENSP00000461969.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000372426|1/8|||1/229|protein_coding||||||ENST00000372426.1:c.1dup|ENSP00000361503.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000372426|1/8|||1/229|protein_coding||||||ENST00000372426.1:c.1dup|ENSP00000361503.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000372426|1/8|||1/229|protein_coding||||||ENST00000372426.1:c.1dup|ENSP00000361503.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000372426|1/8|||1/229|protein_coding||||||ENST00000372426.1:c.1dup|ENSP00000361503.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000372426|1/8|||1/229|protein_coding||||||ENST00000372426.1:c.1dup|ENSP00000361503.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000583037|2/8|||1/204|protein_coding||||||ENST00000583037.1:c.1dup|ENSP00000461969.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above
WARNING: unknown severity for 'frameshift_variant&start_lost&start_retained_variant|atg/aAtg|M/NX|ENSG00000178922|HYI|ENST00000583037|2/8|||1/204|protein_coding||||||ENST00000583037.1:c.1dup|ENSP00000461969.1:p.Met1?|||5.338303|25.8'. using LOW for [u'frameshift_variant', u'start_lost', u'start_retained_variant']
Please report this on github with the effect-string above

vcf2db/7dfc48a

[brentp]

thanks for reporting, can you also share the CSQ or ANN row from the vcf header?

[davemcg]

##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position|BIOTYPE|CANONICAL|DOMAINS|CLIN_SIG|Grantham|MaxEntScan|HGVSc|HGVSp|PUBMED|Phenotypes|CADD_RAW|CADD_PHRED">

Thanks @brentp !

[davemcg]

Happy to give VEP parameters if that is helpful.

[brentp]

can you update your geneimpacts module and retry? I think this might have been fixed a while back.

[davemcg]

Is this a matter of updating the vcf2db install? I'm using this on a cluster. The admins have two versions: 7dfc48a (which I'm currently using) and 1118740.

[brentp]

it's a module that vcf2db uses, just do pip install -U geneimpacts

[davemcg]

That appears to have done it. Thanks @brentp