failed annotation complex variant

[kjass001]

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!

[Kenneth Geerts]

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]

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

cfr commit 344f253

[Wanding Zhou - Bioinformatics]

Thanks for the fix. I merged this change.