inconsistent InFrameInsertion annotation
shannonnana opened this issue · comments
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
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]