inconsistent InFrameInsertion annotation

[shannonnana]

Hi,
Thanks for such a great tool.
I got some inconsistent annotations using gdna and vcf input. Here is a InFrameInsertion example

test.zip
chr7 55248980 Mut C CTCCAGGAAGCCT

the command-line and partial reuslts

$ transvar ganno --refseq --vcf test.vcf
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2284-5_2290dupTCCAGGAAGCCT/. inside_[intron_between_exon_19_and_20]
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2149-5_2155dupTCCAGGAAGCCT/. inside_[intron_between_exon_18_and_19]
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2125-5_2131dupTCCAGGAAGCCT/. inside_[intron_between_exon_19_and_20]
$ transvar ganno -i 'chr7:g.55248981_55248992dupTCCAGGAAGCCT' --refseq --refversion hg19
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2284-5_2290dupTCCAGGAAGCCT/p.A763_Y764insFQEA  inside_[cds_in_exon_20]
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2149-5_2155dupTCCAGGAAGCCT/p.A718_Y719insFQEA  inside_[cds_in_exon_19]
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2125-5_2131dupTCCAGGAAGCCT/p.A710_Y711insFQEA  inside_[cds_in_exon_20]

It looks like that command line version is more reasonable. This was possibly caused by no QueryDUP in vcf version.

Best

[shannonnana]

I converted vcf file to command line form, and got a consistent amino acid annotation as follow:

$ transvar ganno --refseq --vcf test.vcf
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2284-5_2290dupTCCAGGAAGCCT/p.A763_Y764insFQEA  inside_[cds_in_exon_20]
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2149-5_2155dupTCCAGGAAGCCT/p.A718_Y719insFQEA  inside_[cds_in_exon_19]
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2125-5_2131dupTCCAGGAAGCCT/p.A710_Y711insFQEA  inside_[cds_in_exon_20]

$ transvar ganno -i 'chr7:g.55248981_55248992dupTCCAGGAAGCCT' --refseq --refversion hg19
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2284-5_2290dupTCCAGGAAGCCT/p.A763_Y764insFQEA  inside_[cds_in_exon_20]
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2149-5_2155dupTCCAGGAAGCCT/p.A718_Y719insFQEA  inside_[cds_in_exon_19]
chr7:g.55248981_55248992dupTCCAGGAAGCCT/c.2125-5_2131dupTCCAGGAAGCCT/p.A710_Y711insFQEA  inside_[cds_in_exon_20]