Closed kjass001 closed 5 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
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 https://github.com/zwdzwd/transvar/pull/33/commits/344f253ffacebbcbb4381c166a534fd0ccb17f87
Thanks for the fix. I merged this change.
Hi, We annotated vcf of clinical sample with a clinically-relevant insertion exon 20.
Vardict output vcf (marked line 78% VAF):![image](https://user-images.githubusercontent.com/39410349/48057144-95989300-e1b3-11e8-809a-96229c42a438.png)
Transvar annotated and filtered:![image](https://user-images.githubusercontent.com/39410349/48057857-566b4180-e1b5-11e8-9ba9-f0dd2e94249b.png)
-->no annotation. Any options possible to achieve adequate annotation? Thanks for help!