failed annotation complex variant

zwdzwd / transvar

TransVar - multiway annotator for precision medicine

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Closed kjass001 closed 5 years ago

kjass001 commented 6 years ago

Hi, We annotated vcf of clinical sample with a clinically-relevant insertion exon 20.

alignment bwa-mem
variant calling Vardict
annotation TransVar It appears that TransVar cannot annotate following 'complex' mutation (in-frame insertion +adjacent SNV)

Vardict output vcf (marked line 78% VAF):

Transvar annotated and filtered:

-->no annotation. Any options possible to achieve adequate annotation? Thanks for help!

kennethgeerts commented 6 years ago

In case it could help, this is what vardict logs:

[vcf_parse_mutation] warning: Invalid VCF line: chr7 55249013 . A GGTT 371 PASS . GT:DP:VD:AD:AF:RD:ALD 1/0:1302:1019:263,1019:0.7826:263,0:1019,0

mmoisse commented 5 years ago

I solved the issue by changing the definition for MNV from len(ref) > 1 and len(alt) > 1 to len(ref) > 1 or len(alt) > 1

zwdzwd commented 5 years ago

Thanks for the fix. I merged this change.